Re: [gmx-users] gromacs memory usage

Hi Mark and Alexey, Thank you for taking the time to write the responses. Following is the info about the cluster [chou...@hpc-login2 ~]$ uname -a Linux hpc-login2 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux [chou...@hpc2000 ~]$ mpiexec --version Version 0.82

Re: [gmx-users] topol.top

Dear Mark,I have tried the same processing  with version 4.0.5. After that I got the following error messageProgram grompp_s, VERSION 4.0.5Source code file: confio.c, line: 748Fatal error:The spacing of the decimal points in file conf.gro is not consistent for x, y and zMy conf.gro file was constru

Re: [gmx-users] NVT simulation and mdp file

tekle...@ualberta.ca wrote: Hi Justin, Thank you pointing out that! I made all the changes and still cannot go past this line. REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb HETATM1 CB PHE 0 -1.158 0.001 0.000 C HETATM

Re: [gmx-users] NVT simulation and mdp file

Hi Justin, Thank you pointing out that! I made all the changes and still cannot go past this line. REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb HETATM1 CB PHE 0 -1.158 0.001 0.000 C HETATM2 CG PHE 0 -1.158

Re: [gmx-users] topol.top

Dear Mark,I have used version 4.0.3.ZuzanaDňa 03/04/10, Mark Abraham napísal:On 5/03/2010 4:08 AM, Zuzana Benkova wrote:>Dear GROMACS users,>I wanted to do a test calculation on a linear unrealistic molecule PPPBC>without any contributions to energy exept of LJ nonbenoded interactions.>I have pre

Re: [gmx-users] NVT simulation and mdp file

tekle...@ualberta.ca wrote: Hi Justin, It does not work. I eliminated the hydrogen atoms and check the entire .pdb file but could not solve the problem. the modified PDB file. REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb HETATM1 CB PHE 0 -1.15

Re: [gmx-users] NVT simulation and mdp file

Hi Justin, It does not work. I eliminated the hydrogen atoms and check the entire .pdb file but could not solve the problem. the modified PDB file. REMARK This PDB file is created by CS Chem3D REMARK COMPND Tolene.pdb HETATM1 CB PHE 0 -1.158 0.001 0.000

RE: [gmx-users] ethanol bond types

> Thanks David. These are the parameters I added. Do you think they seem > reasonable? You might as well run a simulation yourself, it will be quickly apparent if something is very wrong. Best way to determine these things is try it and see for yourself. Catch ya, Dr. Dallas Warren Drug Deliver

Re: [gmx-users] NVT simulation and mdp file

tekle...@ualberta.ca wrote: Dear Justin, It really help all the feedback you gave me and thank you for that,. I have one issues as well. I try to generate the topology file the way you recommend me using the pdb2gro but failed to get both the topology and gromacs file. This is my Toluene

Re: [gmx-users] topol.top

On 5/03/2010 4:08 AM, Zuzana Benkova wrote: Dear GROMACS users, I wanted to do a test calculation on a linear unrealistic molecule PPPBC without any contributions to energy exept of LJ nonbenoded interactions. I have prepared a topol.top file which I am attaching. After processing this file with

Re: [gmx-users] g_mindist periodic boundary condition

Sorry for the confusion, Tsjerk. Thanks. On Thu, Mar 4, 2010 at 11:47 AM, Tsjerk Wassenaar wrote: > Hi Dian, > > Now why didn't I guess that you were trying on data obtained from > Amber?! Maybe because you didn't explicitly mentioned it. It always > helps to give a full account of what you were

Re: [gmx-users] g_mindist periodic boundary condition

Hi Dian, Now why didn't I guess that you were trying on data obtained from Amber?! Maybe because you didn't explicitly mentioned it. It always helps to give a full account of what you were trying. Anyway, I don't know the format of the top of my head, so you'll have to look in another pdb file an

[gmx-users] topol.top

Dear GROMACS users, I wanted to do a test calculation on a linear unrealistic molecule PPPBC without any contributions to energy exept of LJ nonbenoded interactions. I have prepared a topol.top file which I am attaching. After processing this file with grompp I obtained a message WARNING 1 [file t

Re: [gmx-users] g_mindist periodic boundary condition

Hi Tsjerk, My gromacs is 4.0.4. As it turns out, I do not have a CRYST1 keyword in my pdb file, so I guess the box is not defined yet. The pdb was taken from the trajectory of AMBER simulation, so it starts with the keyword "REMARK". How do I include box dimensions in pdb file then? Just add "CRY

[gmx-users] topol.top

Dear GROMACS users,I wanted to do a test calculation on a linear unrealistic molecule PPPBC without any contributions to energy exept of LJ nonbenoded interactions. I have prepared a topol.top file which I am sending. After processing this file with grompp I obtained a messageWARNING 1 [file topol.

Re: [gmx-users] ethanol bond types

Quoting David van der Spoel : On 3/3/10 8:14 PM, nishap.pa...@utoronto.ca wrote: Hello, I am trying to simulate Ethanol in water using OPLSAA. I already tried it with all atoms, but now I want to try it with United atoms for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I cr

Re: [gmx-users] Multiprotein lipid bilayer

hi justin, will try that thanks Ram On Thu, Mar 4, 2010 at 4:51 PM, Justin A. Lemkul wrote: > > > ram bio wrote: >> >> HI Justin, >> >> Thanks for the info. >> >> I have followed your tutorial earlier, it really works, and that was >> for 1 protein, but if 2 or more different kinds of pro

Re: [gmx-users] Multiprotein lipid bilayer

ram bio wrote: HI Justin, Thanks for the info. I have followed your tutorial earlier, it really works, and that was for 1 protein, but if 2 or more different kinds of proteins are to be inserted then how to generate the a single topology file for all the proteins using pdb2gmx and also can yo

Re: [gmx-users] Multiprotein lipid bilayer

HI Justin, Thanks for the info. I have followed your tutorial earlier, it really works, and that was for 1 protein, but if 2 or more different kinds of proteins are to be inserted then how to generate the a single topology file for all the proteins using pdb2gmx and also can you please let me kno

Re: [gmx-users] Multiprotein lipid bilayer

ram bio wrote: Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please Just about anything is possible :) let me know if any tutorial is available or any kind of help is available

[gmx-users] Multiprotein lipid bilayer

Dear Gromacs Users, I would like to run molecular dynamics by inserting multiple proteins in the same lipid bilayer using gromacs, is it possible? if so, please let me know if any tutorial is available or any kind of help is available Thanks in advance, Ram -- gmx-users mailing listgmx

Re: [gmx-users] harmonic restraints

It is not sure what you mean: if you wonder how it is done in Martini (explained in the paper) or if like to add some yourself. Regular bonds are generally used! On Mar 4, 2010, at 6:15, Ajeeta kaushiki wrote: Dear Sir I am doing a coarse grain MD of a membrane protein using Martini

RE: [gmx-users] GPU GROMACS

Hi, OpenMM can do pbc and it can simulate molecules, so it can also simulate solvents. Berk > Date: Wed, 3 Mar 2010 10:52:54 -0500 > From: j...@drugdiscoveryathome.com > To: gmx-users@gromacs.org > Subject: [gmx-users] GPU GROMACS > > Is anyone working on a build GROMACS with CUDA other than

Re: [gmx-users] harmonic restraints

On 4/03/2010 10:15 PM, Ajeeta kaushiki wrote: Dear Sir I am doing a coarse grain MD of a membrane protein using Martini force field and parameters . In course I am facing problem in understanding " how the harmonic restraints will be applied to mimic secondary structure H- Bonds of the atomic s

[gmx-users] harmonic restraints

Dear Sir I am doing a coarse grain MD of a membrane protein using Martini force field and parameters . In course I am facing problem in understanding " how the harmonic restraints will be applied to mimic secondary structure H- Bonds of the atomic structure to the coarse grain model to maintain s

Re: [gmx-users] g_mindist periodic boundary condition

On 4/03/2010 6:38 PM, Tsjerk Wassenaar wrote: Hi Dian, Which version of gromacs are you using? Can you assert that the pdb file has the correct box? It should have a line starting with CRYST1 (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think) didn't write the CRYST1 record, and

Re: RE: [gmx-users] g_nmeig_d error: can't allocate region

Hi Berk, Thanks for your reply. What is the correct way to compile gromacs in 64 bit mode? I installed fftw-3.0.1. using the following commands ./configure make sudo make install Then I downloaded the gromacs 4.0.7 source code and installed it using the following comman