Re: [gmx-users] Problem in pullx file

On Wed, Aug 4, 2010 at 4:31 PM, Justin A. Lemkul wrote: > > > Aswathy wrote: > >> Dear Gromacs users, >> >> I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. >> Initially I pulled the ligand from extra to intracellular side of the >> protein. The pull code used are given b

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

Nilesh Dhumal wrote: Then it looks there is bug ater define the constraints in itp file, bond distance changes. Then file a bugzilla so the developers can either confirm the bug and fix it, or provide an explanation as to what is going on. -Justin On Wed, August 4, 2010 10:22 pm, Justi

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

Then it looks there is bug ater define the constraints in itp file, bond distance changes. On Wed, August 4, 2010 10:22 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Its oscillate between +/- 3-4 A. >> If I freeze the distance by using freeze groups and dim in mdp file. It >> works

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

Nilesh Dhumal wrote: Its oscillate between +/- 3-4 A. If I freeze the distance by using freeze groups and dim in mdp file. It works perfectly for NVT simulations. It oscillate for NPT simulation. I don't know if there have been any changes (I don't see anything in the revision history), but

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

Its oscillate between +/- 3-4 A. If I freeze the distance by using freeze groups and dim in mdp file. It works perfectly for NVT simulations. It oscillate for NPT simulation. Nilesh On Wed, August 4, 2010 9:56 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> constraints = all-bonds is

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

Nilesh Dhumal wrote: constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. So you used g_dist to determine the distances with the setup shown below, but did you correct for PBC effects? Is

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

constraints = all-bonds is working. I have solvent molecule for which I don't want constraints on them. I can't use constraints = all-bonds for simulation. Nilesh On Wed, August 4, 2010 9:48 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello >> I am trying to constraints of a bond.

Re: [gmx-users] frezzing a bond : NPT and NVT simulations

Nilesh Dhumal wrote: Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Maybe there's a bug in the interpretation of the constraints? The combination

[gmx-users] frezzing a bond : NPT and NVT simulations

Hello I am trying to constraints of a bond. I checked the distance using g_dist, distance changes from 3.5 A to ~ 8.0A. Can anyone tell why it changes. Here I have pasted mdp file and itp file. Nilesh Solvent.itp ; Derived from parsing of runfiles/alat.top.orig [ defaults ] ; nbfunccomb-rul

[gmx-users] Re: Resilin Project

You've basically got the idea. As a subtle point, the "strength" of a method is completely user-defined (by the tau_p parameter, how frequently the temperature is coupled). No one method is "stronger" than another, but it is correct to say that the Nose-Hoover thermostat produces a rigorous

Re: [gmx-users] Force field parameters for the heme in ff53a6

It appears that the parameters in 53a6 are unchanged relative to 43a1, the reference for which is the GROMOS manual. Unfortunately, you have to pay the licensing fee to obtain the manual. There are certainly several literature references for various aspects of the GROMOS functional form and

[gmx-users] Force field parameters for the heme in ff53a6

Hi, All, Does anyone know where the force field parameters for the heme in the ff53a6 force field were obtained? Much appreciated, Art Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing list

Re: [gmx-users] Intermolecular RDF in DPPC

prithvi raj pandey wrote: Dear gmx users, I want to calculate intermolecular RDF between N and carbonyl oxygen atoms in a DPPC bilayer. As suggested in some mails in the mailing list i wanted to generate one tpr file for the purpose containing exclusion 49 (as united atom model of DPPC cont

[gmx-users] Intermolecular RDF in DPPC

Dear gmx users, I want to calculate intermolecular RDF between N and carbonyl oxygen atoms in a DPPC bilayer. As suggested in some mails in the mailing list i wanted to generate one tpr file for the purpose containing exclusion 49 (as united atom model of DPPC contains 50 atoms). But while generat

Re: [gmx-users] Tabulated potentials and performance

Hi guys, >From what I've tested, it seems that performances decreases linearly with the amount of tables used, exactly the opposite of what Lanyuan has said. I've tested this for GROMACS 4.0.4 and from 1 to 190 tables. Near 190 tables, it seems that a threshold in performance starts to form, but n

Re: [gmx-users] tests for gmx 4.5

I'm glad there's some interest in the test set. I'm happy to update what I did for 4.0.7 for 4.5 also, but there are a number of issues that need attention from someone other than me. I listed those that occurred to me here http://lists.gromacs.org/pipermail/gmx-developers/2009-August/003586.htm

[gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

Dear Szilárd and Rossen: I have attempted with gcc4.4.0 and I got the same result. I can verify that cmale/FindCUDA.cmake exists and contains the MARCO for CUDA_INCLUDE_DIRECTORIES but it seems that this library is not, for some reason, getting loaded in by at least kernel/gmx_gpu_utils/C

Re: [gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

Hi Chris, Though I'm repeating myself, for the sake of not leaving this post unanaswered (btw reposts should be avoided as much as possible!): First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake script from the 2.

Re: [gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

Hi Chris, First of all, as Rossen said, the <=2.6.4 is a typo, it was meant to be >=2.6.4, it _should_ work with 2.8.0 (I took the FindCUDA.cmake script from the 2.8 cmake sources :), but... icc is _not_ supported by CUDA, AFAIR some people reported getting it work but only in some very limited

Re: [gmx-users] Problem in pullx file

Aswathy wrote: Dear Gromacs users, I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. Initially I pulled the ligand from extra to intracellular side of the protein. The pull code used are given below. pull = umbrella pull_geometry= dis

Re: [gmx-users] Can I make make_ndx interactive?

Jennifer Williams wrote: Hi, Is there some way of making the make_ndx file interactive so that I can include it in a script? I would usually type in "a C_O and O_C" to select my atoms I've tried altering the example on the webpage for making commands interactive: make_ndx -flags < try:

RE: [gmx-users] Precision in trajectory file

From: mark.abra...@anu.edu.au To: gmx-users@gromacs.org Date: Wed, 4 Aug 2010 12:56:54 +1000 Subject: Re: [gmx-users] Precision in trajectory file - Original Message - From: Inon Sharony Date: Tuesday, August 3, 2010 20:55 Subject: [gmx-users] Precision in trajectory file To: "gmx-us

Re: [gmx-users] tests for gmx 4.5

Hi, The tests haven't been ported to 4.5 yet but I hope to fix that before the final release. Rossen On 7/31/10 7:08 PM, Alan wrote: Is there a proper set of tests for gmx 4.5 because neither ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or "git clone git://git.gromacs.org/regressionte

Re: [gmx-users] gmx 4.5 configure options confusing

Hi, This was a typo in configure.ac, the second line should say --without-qmmm-orca. Fixed it for the next release. Thanks for reporting. Rossen On 7/31/10 12:11 PM, Alan wrote: For gmx 4.5 beta, I see with ./configure --help: --without-qmmm-mopacUse modified Mopac 7 for QM-MM (see

[gmx-users] Problem in pullx file

Dear Gromacs users, I am doing SMD of a ligand pathway, and then want ot do the PMF analysis. Initially I pulled the ligand from extra to intracellular side of the protein. The pull code used are given below. pull = umbrella pull_geometry= distance pull_dim