[gmx-users] how to remove an energy contribution in gromacs?
Jones de Andrade
johannesrs at gmail.com
Mon Aug 6 16:40:13 CEST 2007
So, this means:
nstxtcout from 10 to 1
nsteps from 100000 to 10000
nstlog from 10 to 1
nstenergy from 10 to 1
nstlist from 5 to 1.
This is what should be changed in the .mdp file in order to get a proper
rerun g_energy analysis?
@Berk: Thanks a lot for the clarification. But still could not understand
why there is any need for using g_analyze. Could you ple clarify this point
out for me?
Thanks a lot for everybody in advance!
On 8/6/07, Xavier Periole <X.Periole at rug.nl> wrote:
> You should also update your neighbor list every step (10ps). if you
> the original 5/10 steps frequency mdrun -rerun will update them every
> 5/10*10ps ...
> >>From: "Jones de Andrade" <johannesrs at gmail.com>
> >>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >>Subject: Re: [gmx-users] how to remove an energy contribution in
> >>Date: Mon, 6 Aug 2007 11:13:44 -0300
> >>Hi both.
> >>@ Mark: thanks mark. Have to admit that I haven't thought about the
> >>exclusions possibility. Specially because I was looking for a simple way
> >>doing it without removing the dynamics related to these forces from the
> >>simulation itself. So, changing the nexcl looked a bit easier to do.
> >>@ Berk:
> >> > This seems the right approach to me.
> >> >
> >> > I don't know what you are doing exactly.
> >> > But are you aware that the averages in g_energy and in the log file
> >> > are using every integration step, whereas with rerun you only get
> >> > for every frame in your trajectory?
> >> > I think the averages of mdrun -rerun are still incorrect, you need to
> >> > the average of the values in the energy.xvg file.
> >> Ok, let me see if I understood: This means that, if I simulated
> >>with the .mdp saying for the system to save the trajectory every 10 time
> >>steps, and even with this fact still mentioned in the .mdp file for the
> >>"mdrun -rerun" job, it would barelly mean that the energies would be
> >>by a factor of 10, and the "oscilations" are due to the reduction in the
> >>statistics? Is it correct?
> > Yes.
> > The factor will not be exactly 10 though, since there are some end
> > With may frames it will be very close to 10 though.
> >>So, the proper way of doing if is not just keep on saying on the .mdp
> >>that it's saved every 10 time steps, but rather more or I just get the
> >>results and multiply them by 10, or make the rerun informing a 10 times
> >>larger time-step?
> > You can not fix the problems caused by this "bug".
> >For the average values of the rerun you should just run g_energy
> > and extract the average from the energy.xvg file using for instance
> > Berk.
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> XAvier Periole - PhD
> 1- Institute of Molecular Assemblies
> City University of New York - USA
> 2- Molecular Dynamics-Group
> University of Groningen - The Netherlands
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