Re: [gmx-users] energy minimization problem

On 11/3/13 6:20 AM, kiana moghaddam wrote: Dear Justin Further to your previous email, I want to calculate free energy for DNA-ligand interaction. According to your answer, for more sensitive calculations like free energy simulations and normal modes, emtolshould be lower than 1. As I

Re: [gmx-users] energy minimization problem

On 11/2/13 3:38 PM, kiana moghaddam wrote: Hi GMX Users I 'm running MD Simulation for DNA-ligand interaction. I ran energy minimization with emtol=10, 100 and 250 in 1 steps (steepest descent followed by the conjugate gradient algorithm). The lowest value for energy obtained for

RE: [gmx-users] energy minimization problem

Actual text input / output would be a good idea here. What is the actual output when you try to run it the second time? Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010

RE: [gmx-users] Energy minimization problem with Double precision and mpi

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote

Re: [gmx-users] Energy minimization problem with Double precision and mpi

Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah

RE: [gmx-users] Energy minimization problem with Double precision and mpi

I managed to install mdrun_d from CVS and the problem is fixed -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Josiah Zayner Sent: Saturday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [gmx-users] Energy minimization problem with Double

RE: [gmx-users] Energy minimization problem with Double precision and mpi

-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah Zayner wrote: I

Re: [gmx-users] Energy minimization problem(1-4 interaction at distance 3.540 is larger than the 1-4 table size 1.000 nm)

Hi Arun, You have to get your methods straight.., and be more clear in the phrasing of your question. I am trying to simulate a surfactant-water system(also contains some co-surfactants). Surfactant is a cationic surfactant with chloride as counterion. And the

Re: [gmx-users] Energy Minimization problem

19 apr 2007 kl. 03.45 skrev Venky Krishna: Hi George, I usually delete/move the molecules reported to have high force values in the minimization steps. A better thing would be to start with a box which has sufficient intermolecular distance again by deleting molecules which are very

Re: [gmx-users] Energy Minimization problem

Thanks guys for your replies. The problem is that the potential energy is too low: it can't be true I think. Also, the high force means that the system is not really stable (at least the atom influenced by this force is not!). And yes I defined flexible for the water molecules. I don't know if

Re: [gmx-users] Energy Minimization problem

George Abadir wrote: Thanks guys for your replies. The problem is that the potential energy is too low: it can't be true I think. Also, the high force means that the system is not really stable (at least the atom influenced by this force is not!). And yes I defined flexible for the water

Re: [gmx-users] Energy Minimization problem

Hi George, I usually delete/move the molecules reported to have high force values in the minimization steps. A better thing would be to start with a box which has sufficient intermolecular distance again by deleting molecules which are very close to each other (use the g_mindist program)

Re: [gmx-users] Energy Minimization Problem

On Mon, 17 Apr 2006 08:21:35 -0400 (EDT) Robson P. S. Peguin [EMAIL PROTECTED] wrote: Hi everybody, I'm trying to simulate an interfacial system using Gromacs. My simulation box has water in one side and hydrofluorocarbon in the other side. This system was successfully tested using DL-POLY