Re: Help building a desktop for namd. From: Gianluca Interlandi (gianluca_at_u. washington. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallNext in thread: Gianluca Interlandi: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. 26588. edu> > wrote: > Roy, > > I think that you are confusing two things. My> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit :Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. Interlandi G. Education/training Institution and location Dates attended Degree Conferred Field of study Interlandi G, Thomas WE. Gianluca Interlandi 1 , Minhua Ling, An Yue Tu, Dominic W Chung, Wendy E Thomas Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, United States of America. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. From: Buddhadev Maiti (bmaiti_at_gsu. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. It's > slightly faster but still not that much faster than running on 16 CPU cores. From: Gianluca Interlandi (gianluca_at_u. 7b4 is thatRE: DCD. From: Gianluca Interlandi (gianluca_at_u. Cheers! If you are looking for Virtual General Counsel, please go to: out professional insights posted by Isabella Interlandi, Attorney at Law, Legal adviser, UNSC 1540 Committee former Expert, Customs legislation and procedures. The more tasks you have the > more frequently the CPUs need to update each other. edu>: > Dear NAMD users, > > Is it possible to perform Poisson Boltzmann calculation with NAMD? > > I have simulated the wildtype and a single-point mutant of a protein. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. edu: "Re: high (or low) pressure readings" Next in thread: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Brian Bennion: "Re: fatal error"> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread:. edu) Date: Wed Sep 23 2015 - 13:37:27 CDT Next message: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Previous message: Mayne, Christopher G: "Re: FFTK Bond optimization" In reply to: Gianluca Interlandi: "SSD vs SSHD vs mechanical" Next in thread: Gianluca Interlandi: "Re:. From: Gianluca Interlandi (gianluca_at_u. Policies. NAMD doesn't that i know of. 0 and 2. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino:. From: Gianluca Interlandi (gianluca_at_u. edu> > Date: Monday, May 7, 2007 7:26 pm > Subject: Re: namd-l: query about wrapped coordinates > > > I have actually found a much easier way of adding the crystal > > information > > to your trajectory. washington. Next in thread: Gianluca Interlandi: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. On Thu, Apr 09, 2015 at 03:39:49PM -0700, Gianluca Interlandi wrote: > Dear list, > > Starting with version 1. -Fatemeh On Fri, Dec 3, 2010 at 2:08 PM, Gianluca Interlandi < gianluca_at_u. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. From: John Stone (johns_at_ks. , the force on the SMD atom gets huge. washington. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. See more properties from this host. 1 the measure command of VMD can also > calculate the energy: > > energy energy_term atom_list [parameters] [options]: Returns the > specified energy term for a given set of atoms. In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. mx: "Re: Fat node" Previous message: Dan Strahs: "checkpoint software for NAMD?" In reply to: Dan Strahs: "checkpoint software for NAMD?". Choose File -> Save Coordinates. washington. washington. washington. at 298. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. washington. Reply: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] Dear NAMD users, A portion of my protein is outside of the simulation box. 7 ns/day, which seems decent given the system size. The structure was derived from the complex co-crystallized with botrocetin (PDB code 1U0N) (), because this is the only structure of the complex where 11 amino acids of the A1 N-terminal linker were resolved (other structures. University of Washington Department of Bioengineering. washington. Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. g. uiuc. From: Gianluca Interlandi (gianluca_at_u. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. washington. Thomas, 2 , * and Evgeni V. From: Gianluca Interlandi (gianluca_at_u. 7 out the door on Friday. You should simulate it in explicit water (or try one of the implicitGianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. g. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. Search for: Main Menu. SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. PMID: 37700555; DOI: 10. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field > From: Gianluca Interlandi <gianluca_at_u. There have been over 180 downloadsReply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Bidet · Toilet · Shower. From: Gianluca Interlandi (gianluca_at_u. Sokurenko 1 , *. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. One of the two proteins has reached one of > the boundaries of the box and it has been wrapped around. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. washington. 26588 Item in Clipboard Cite. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. You should simulateCorresponding Author. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in. washington. washington. edu) Date: Tue Nov 01 2011 - 14:14:51 CDT Next message: Gianluca Interlandi: "Re: rlwrap problem on" Previous message: Joshua A. Previous message: Gianluca Interlandi: "stepspercycle" In reply to: Gianluca Interlandi: "stepspercycle" Next in thread: Gianluca Interlandi: "Re: AW: stepspercycle" Reply: Gianluca Interlandi: "Re: AW: stepspercycle" Messages sorted by: [ attachment ] No idea where you were looking, but this parameter is still fundamental for. You should simulate it in explicit water (or try one of the implicitOn Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). 2020-10-26T08:31:24-07:00 September 9th, 2014 | Read More UW Bioengineering Summer Camp 2014 concludes, teaches high school students about bioengineering, global health. Re: Protein in/out of box. I'm > not sure whether the CHARMM program can read. I needed to install the 'patch' program. Just a good MD toy ! Victor owner-namd-l_at_ks. edu) Date: Wed Sep 18 2013 - 13:53:55 CDT Next message: Axel Kohlmeyer: "Re: Open VMD from a remote host" Previous message: Gianluca Interlandi: "Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Axel Kohlmeyer:. It's > slightly faster but still not that much faster than running on 16 CPU cores. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. Re: Langevin process in NAMD tutorial"Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. Michel Espinoza-Fonseca: "Re: Vibrational. uiuc. Previous studies. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. washington. Choose File -> Save Coordinates. washington. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. Join Facebook to connect with Gianluca Interlandi and others you may know. From: Gianluca Interlandi <gianluca_at_u. washington. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. 6 version, although I am not running the cluster at full load yet. Citat Gianluca Interlandi <gianluca_at_bioc. Stenkamp, 3 Wendy E. washington. by G. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Location info. washington. washington. First of all, I am sorry to bother you again for problem. Does it also take account of the Urey-Bradley term? Many thanks, Gianluca ----- Gianluca Interlandi gianluca_at_bioc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. washington. The simulations were not performed at constant velocity > but at constant force. From: Gianluca Interlandi (gianluca_at_u. washington. It's > slightly faster but still not that much faster than running on 16 CPU cores. I thought I will see in my output file the energies stored at times 0 fs, 500 fs,. gianluca@u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Eric Klavins Professor. txt". uiuc. I did what you and Gianluca suggested but still have two caveats. washington. FimH consists of a pilin domain (PD) that anchors it to the rest of the fimbria and an allosterically regulated le. On 6 May 2009, at 11:04, Gianluca Interlandi wrote: > Thanks Anton for your answer. washington. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". edu> wrote: In reply to: Gianluca Interlandi: "Compiling NAMD 2. upenn. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. Re: Abe versus Lincoln. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. (did you see if any hunk failed?) Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. eduRe: Question about equilibration. washington. washington. Sarah Keller Professor. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. 7 released" Messages sorted by: [ attachment ] Hi all, I pushed 2. On Tue, Jul 10, 2012 at 1:14 PM, Gianluca Interlandi < gianluca_at_u. washington. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. 7b1 on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallIn reply to: Gianluca Interlandi: "Compiling NAMD 2. 0 and 2. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. C; the more troublesome part is the lack of long-range electrostatic treatments. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. washington. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. In reply to: Gianluca Interlandi: "Compiling NAMD 2. Facilities. edu> wrote: > Roy, > > I think that you are confusing two things. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. edu> wrote: > Hi, > > Can the current version of NAMD be used together with the new CHARMM36 force > field? The parameter files are "top_all36_prot. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. Just source the Tcl file and use the 'unwrap' procedure. washington. In the text > field you can enter your atom selection, e. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Electrical. Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. From: Gianluca Interlandi [gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"From: Gianluca Interlandi (gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Sep 21 2006 - 16:55:46 CDT Next message: jonathan_at_ibt. running multicore version on a 2-CPU node. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. E-mail: [email protected] > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. From: Gianluca Interlandi (gianluca_at_u. 7 out the door on Friday. washington. Join Facebook to connect with Gianluca Interlandi and others you may know. washington. Just a good MD toy ! Victor owner-namd-l_at_ks. From: Stern, Julie (jvstern_at_bnl. Friend and Aachal Jalan and Shivani Gupta and Gianluca Interlandi and Yan Liu* and Veronika Tchesnokova. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. edu> Cc: <namd-l_at_ks. washington. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. E-mail: [email protected],. SMD on center of mass. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. Department of Bioengineering, University of Washington, Seattle, Washington, 98195. washington. 20-23 2012)<br><br>2001 May/2002 September: Master in Tourism Management - Academy of Trade and Tourism, Trento, Italy (1900 hrs). edu on behalf of Gianluca Interlandi [gianluca_at_u. Thanks for the reply. From: Gianluca Interlandi (gianluca_at_u. . >From: Gianluca Interlandi (gianluca_at_u. MyGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. a, three-dimensional structure of the complex between A1 and GpIbα used in this manuscript. Author Profile. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. That's why one wants to use a low value for the damping constant, in principle. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. I want to simulate a protein > attached to mannose. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. This is unrelated to KDE3. Anton. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. In this way, you could get a feeling what NAMD can do before you > invest money. washington. edu> wrote: > Hi Fatemeh, > > Thanks for replying. washington. Proteins. One of the. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. washington. Jessica is a seasoned litigator, having graduated from the. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. Display options. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. uiuc. Michel Espinoza-Fonseca: "Re: Vibrational. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi! Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. From: Gianluca Interlandi (gianluca_at_u. 5923 Kcal/mol also we have 6. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. washington. VMD-L Mailing List. Re: How to unsubscribe ? From: Gianluca Interlandi (gianluca_at_u. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. Gianluca Interlandi [email protected] orcid. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. Just source the Tcl file and use the 'unwrap' procedure. (2010) The catch bond mechanism between von Willebrand factor and platelet surface receptors investigated by molecular dynamics simulations. Fwd: Installing NAMD on windows. edu, Tel: (206) 685 4435, Fax: (206) 685 3300 1. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. From: Mitchell Gleed (aliigleed16_at_gmail. The Netherlands) is an antibody raised against K12 FimH-lectin domain (residues 1–160) and previously determined to recognize or induce the high affinity state of K12 FimH, especially in the presence of ligand ( buffer in wells of 96-well flat-bottom plates at 37 °C for 1 h. 7 ns/day, which seems decent given the system size. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. From: Gianluca Interlandi (gianluca_at_u. Choose File -> Save Coordinates. 97 pN*nm = 1 Kcal/mol In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). edu) Date: Thu Nov 02 2006 - 21:27:41 CST Next message: Dhiraj Srivastava: "production in NVE ensemble after equilibration in NPT ensemble" Previous message: Gianluca Interlandi: "Re: SMD on center of mass" In reply to: Gianluca Interlandi: "Re: SMD on center of mass""wrapAll on" with a complex. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Wed Sep 29 2010 - 16:34:24 CDT Next message: Gianluca Interlandi: "Re: Re: Experience with Asus Netbook" Previous message: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" In reply to: TRINH Minh Hieu: "Re: Re: Experience with Asus Netbook" Next in. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"Previous message: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" In reply to: Aron Broom: "Re: Am I doing the Right Thing?" Next in thread: Aron Broom: "Re: Am I doing the Right Thing?" Reply: Aron Broom: "Re: Am I doing the Right Thing?" Messages sorted by: [ attachment ] Hi Aron, I understand now what you are. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. washington. Re: replica exchange and GPU acceleration. edu Phone: (206)685-4435 Office: Foege N430 E Gianluca Interlandi I am interested in understanding at molecular level the function of proteins involved in hemostasis and thrombosis, and how they interact with each other and with material surfaces. Michel Espinoza-Fonseca: "Re: Vibrational. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. washington. washington. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. /night - Ortigia - Amenities include: Internet, Air conditioning, TV, Satellite or cable, No smoking Bedrooms: 1 Sleeps: 3 Minimum stay: 2 night(s) Book online - Book holiday rental 11131246 with Vrbo. washington. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu) Date: Thu Nov 02 2006 - 15:40:40 CST Next message: Gianluca Interlandi: "Re: SMD on center of mass" Previous message: Ugur Akgun: "ABF on a single molecule" In reply to: Gianluca Interlandi: "Re: external force" Next in. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. washington. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. double. edu> > wrote: From: Gianluca Interlandi [gianluca_at_u. uiuc. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. washington. washington. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Gianluca Interlandi composed on 2017-01-23 13:40 (UTC-0800):. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. There have been over 180 downloads and no complaints so far. I needed to install the 'patch' program. edu. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. The simulations were not performed at constant velocity > but at constant force. Facebook gives people. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. washington. washington. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. Re: Vibrational mode analysis. Gianluca On Thu, 31 May 2012, Kapil jain wrote: > Hi all, > I am running md simulation on homology model of a membrane protein, following the membrane > protein tutorial. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca InterlandiReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. edu) Date: Wed Dec 12 2012 - 14:49:46 CST Next message: JC Gumbart: "Re: NAMD and new FF CHARMM36" Previous message: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" In reply to: Evgeny Bulat: "Re: NAMD and new FF CHARMM36" Next in thread: Jeffrey Potoff: "Re: NAMD and new FF CHARMM36" > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field > parameters? > > Thanks, > Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" Next in thread: Gianluca Interlandi: "Re: query about wrapped coordinates" Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. From: Gianluca Interlandi (gianluca_at_u. edu > Betreff: Re: namd-l: Mysterious slow down in parallel > > You should read about domain decomposition. edu> > wrote: > are other people also using those GPUs? > > > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. edu) Date: Wed Aug 05 2009 - 13:19:25 CDT Next message: Gianluca Interlandi: "Re: SMD output : which col represents force, second or last" Previous message: David Tanner: "Re: SMD output : which col represents force, second or last" In. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. FimH. We are building a smaller cluster though in the lab and will test the scalabilityGianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. ca) Date: Tue Oct 31 2023 - 20:31:14 CDT Next message: Gianluca Interlandi: "Re: VMD openGL over ssh from a server with NVIDIA" Previous message: Victor Kwan: "Re: VMD openGL over ssh from a server with NVIDIA" In reply to: Gianluca Interlandi: "Re: VMD openGL over ssh from a. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. washington. 97 pN*nm = 1 Kcal/molIn reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. 7 with the PLUMED patch" Messages sorted by: [ attachment ] Hi Gianluca, My guess is that something went wrong while patching namd with plumed. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. From: Axel Kohlmeyer (akohlmey_at_gmail. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. > > According to your banchmarks, it looks like the less expensive GTX285. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Correspondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. edu] Sent: Friday, June 17, 2016 2:29 PM To: Richard Wood Cc: John Stone; vmd-l_at_ks. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. washington. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Re: Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. washington. From: Gianluca Interlandi (gianluca_at_u. e. . edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u.