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 understa

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 emtol=

[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 minimiz

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&q

[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 a

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

> -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 &g

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: 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

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: >

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

urday, June 23, 2007 1:05 PM To: gmx-users@gromacs.org Subject: [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

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 cha

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 cosurfac

[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 surfactan

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 mole

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

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 clos

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)

[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

[gmx-users] Energy minimization problem with macromolecule and polarizable water model

Hello, I recently obtained (from DvS) the .itp file for the SSWM4-DP polarizable water molecule, and a corresponding set of water box coordinates. I use double precision executables in all of the calculations mentioned below. I ran an energy minimization on this box of water, then a 500ps

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-PO

Re: [gmx-users] Energy Minimization Problem

Robson P. S. Peguin 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 simulation package previously. Also, the box containing pure

[gmx-users] Energy Minimization Problem

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 simulation package previously. Also, the box containing pure hydrofluorocarbon worked fin