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

[gmx-users] energy minimization problem

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 emtol=10.  I have some questions about energy

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

[gmx-users] energy minimization problem

Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am trying to energy minimize the structure , in vaccum.( in double precision) , but am not able

RE: [gmx-users] energy minimization problem

February 2010 12:06 AM To: gmx-users@gromacs.org Subject: [gmx-users] energy minimization problem Hi , I have a protein with 2 chains. I need to do normal mode analysis on it. As there are no covalent bonds between the two chains, I did not use the merge option in the pdb2gmx command. I am

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

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

Each time I try to run mdrun with double precision and more than one node, I always receive some atom with infinite Fmax, no matter what I do, Always on Step=0. The strangest thing is that it still attempts the minimization but the values never change except for Dmax in a steepest descent. If I

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

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

Dear gmx-users: 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 cosurfactant is fatty alcohol. water is of spc model. I got topologies from Prodrg for my

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

[gmx-users] Energy Minimization problem

Hi, I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following message: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 Double precision normally

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