Re: [gmx-users] compatibility of MOPAC charges with GROMACS ?

On Wed, May 16, 2007 at 05:16:49PM -0700, David Mobley wrote: > >So what you really need to do, once you have worked out which forcfield > >you are going to use, go back to the documentation / papers for that > >particular forcefield, see how they generated the parameters, then use > >that same pro

[gmx-users] error in topology file generation

*hello everybody,* *i am new user to GROMACS,* *i want to perform simulations on docked protein ligand complex,* *During the conversion of the PDB file i came to such a problem: **just before the end of conversion the program pdb2gmx.exe told that my **PDB file compound is not included into Groma

[gmx-users] Re: Error while doing EM in DMSO.

Dear David, Thanks for advice, i had made the changes but still getting the same error that Fatal error: Atomtype 'SD' not found! SDMSO 32.06000 ; DMSO Sulphur (solvent) CDMSO 15.03500 ; DMSO Carbon (solvent) ODMSO 15.99940 ; DMSO Oxygen (solvent) **Changes Made in ff

[gmx-users] Compiling Gromacs on 64 bit windows platform...

Hi guys, I am trying to compiler GROMACS onto 64 bit windows platform with AMD Opteron Machine with Windows 2003 Server R2. It may sound pretty basic but i am not able to figure out... I could see assembly code in nonbonded directory and i am trying to write makefile to build the same but i am

Re: [gmx-users] error in topology file generation

Archana Chavan wrote: /hello everybody,/ /i am new user to GROMACS,/ /i want to perform simulations on docked protein ligand complex,/ /During the conversion of the PDB file i came to such a problem: //just before the end of conversion the program pdb2gmx.exe told that my //PDB file compound is

Re: [gmx-users] Re: Error while doing EM in DMSO.

Anil Kumar wrote: Dear David, Thanks for advice, i had made the changes but still getting the same error that Fatal error: Atomtype 'SD' not found! SDMSO 32.06000 ; DMSO Sulphur (solvent) CDMSO 15.03500 ; DMSO Carbon (solvent) ODMSO 15.99940 ; DMSO Oxygen (solvent)

[gmx-users] FEP with real or dummy charges?

Hi I want to calculate the change in free energy (electrostatic contribution only) when introducing a charge in a certain site of a protein using a single step FEP. Should this be done with charging an inserted virtual site (a dummy atom) or a protein atom (e.g. Ca)? I noticed that in the

[gmx-users] how to increase the number of

Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes un

[gmx-users] question about g_rmsdist II

Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! Thanks, Fabrizio --- Messaggio inoltrato --- Da: Fabrizio Mancinelli <[EMAIL PROTECTED]> A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all,

Re: [gmx-users] how to increase the number of

Afonso Duarte wrote: Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the num

Re: [gmx-users] question about g_rmsdist II

Fabrizio Mancinelli wrote: Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! If you don't get any luck, remember that the source code is available for a reason :-) --- Messaggio inoltrato --- Da: Fabrizio Mancinelli <[EMAIL PROTECTED]> A: g

Re: [gmx-users] Compiling Gromacs on 64 bit windows platform...

Kedar Potdar wrote: Hi guys, I am trying to compiler GROMACS onto 64 bit windows platform with AMD Opteron Machine with Windows 2003 Server R2. It may sound pretty basic but i am not able to figure out... I could see assembly code in nonbonded directory and i am trying to write makefile t

Re: [gmx-users] Compiling Gromacs on 64 bit windows platform...

I think, i forgot to mention that i am trying to compile GROMACS on native windows and not on Cygwin... On 5/17/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Kedar Potdar wrote: > Hi guys, > > I am trying to compiler GROMACS onto 64 bit windows platform with AMD > Opteron Machine with Windows 200

Re: [gmx-users] same simulation, different results

Shutting off the fft optimization produced the same results for 3.2.1. Then I tried running two simulations using version 3.3.1 with the optimized fft and they differed. Your response seemed to imply that the newer version should produce identical results. Could you clear this up for me?

Re: [gmx-users] same simulation, different results

Jim Fonseca wrote: Shutting off the fft optimization produced the same results for 3.2.1. Then I tried running two simulations using version 3.3.1 with the optimized fft and they differed. Your response seemed to imply that the newer version should produce identical results. Could you clear

Re: [gmx-users] question about g_rmsdist II

17 maj 2007 kl. 15.49 skrev Mark Abraham: Fabrizio Mancinelli wrote: Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! If you don't get any luck, remember that the source code is available for a reason :-) --- Messaggio inoltrato ---

[gmx-users] bondtype 5

This may be a really simple question, I know, but still... How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards): WARNING 1 [file "e

Re: [gmx-users] bondtype 5

Nicolas Schmidt wrote: This may be a really simple question, I know, but still... How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwa

[gmx-users] problem with genion

Hi gromacs-users, I have a problem with the simulation of a capped lysine residue.I followed the tutorial step by step. I added 1 Cl ion into my system in order to neutralize the overall charge by using genion, and then used the grompp command and I encountered with the following error: Progra

[gmx-users] initial configuration problems and energy minimization

Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counter

[gmx-users] Calculate individual force between each atom pair

Hi, Everyone, The force given by .trr file is the total force acted on each atom. Now I would like to modify codes to calculate individaul force between each atom pair. Is it possible in gromacs? (Because I remember some part of gromacs is writen in Fortran and already compiled). Thanks in advan

Re: [gmx-users] bondtype 5

By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this? Have you tried looking at the bottom of your normal output? Mark ___ gmx-users mailing list

Re: [gmx-users] problem with genion

OZGE ENGIN wrote: Hi gromacs-users, I have a problem with the simulation of a capped lysine residue.I followed the tutorial step by step. I added 1 Cl ion into my system in order to neutralize the overall charge by using genion, and then used the grompp command and I encountered with the foll

Re: [gmx-users] initial configuration problems and energy minimization

Arun kumar wrote: Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(

Re: [gmx-users] Calculate individual force between each atom pair

WU Yanbin wrote: Hi, Everyone, The force given by .trr file is the total force acted on each atom. Now I would like to modify codes to calculate individaul force between each atom pair. Is it possible in gromacs? (Because I remember some part of gromacs is writen in Fortran and already compi

Re: [gmx-users] Compiling Gromacs on 64 bit windows platform...

Kedar Potdar wrote: I think, i forgot to mention that i am trying to compile GROMACS on native windows and not on Cygwin... That's going to make it hard to interest people in helping you, since probably nobody has done that before, and with the availability of cygwin few people have an incent

Re: [gmx-users] how to increase the number of

On 5/17/2007 8:14 PM, Afonso Duarte wrote: Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any w

Re: [gmx-users] how to increase the number of

Hi Afonso, An easier way would be to use the -time flag with grompp. it would basically set the first time frame for the new tpr to what you give it. jus play around with it and i'm sure you can get what you wanted. dont forget to include the -np flag of course. :) hope this helps. Kota. On 5/1

[gmx-users] energy minimization - double precision

Dear users, I'm trying to minimize the energy of a protein in vacuum. I have restrained the backbone with posre.itp generated using genpr. when i try to minimize the energy of this protein using single precision grompp followed by an mdrun, it does not converge even after 600 steps and returns say

Re: [gmx-users] energy minimization - double precision

Pradeep Kota wrote: Dear users, I'm trying to minimize the energy of a protein in vacuum. I have restrained the backbone with posre.itp generated using genpr. when i try to minimize the energy of this protein using single precision grompp followed by an mdrun, it does not converge even after 6

Re: [gmx-users] how to increase the number of

Pradeep Kota wrote: Hi Afonso, An easier way would be to use the -time flag with grompp. it would basically set the first time frame for the new tpr to what you give it. jus play around with it and i'm sure you can get what you wanted. dont forget to include the -np flag of course. :) No, t

Re: [gmx-users] how to increase the number of

Oops ! am sorry. but i'm sure i had done this once earlier with some flag, without tinkering with the mdp file. i vaguely remember doing that. shall verify and get back to you. sorry afonso, and thanks for pointing out, mark ! :) regards, Kota. On 5/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote

Re: [gmx-users] initial configuration problems and energy minimization

Hi Mark. Thanks for your suggestions I will use your suggestions to solve the problem. And then I will reply here about the outcomes. Regards Arun On 5/18/07, Mark Abraham <[EMAIL PROTECTED]> wrote: Arun kumar wrote: > Dear gmx-users, >Here I h

[gmx-users] glibc error with g_density (only for some cases)

Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I

Re: [gmx-users] glibc error with g_density (only for some cases)

Arun kumar wrote: Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations