[gmx-users] how to remove an energy contribution in gromacs?

[Xavier Periole]

> nstxtcout from 10 to 1
> nsteps from 100000 to 10000
> nstlog from 10 to 1
> nstenergy from 10 to 1

Only nstlist needs to be changed.
> nstlist from 5 to 1.

The other ones don't need to be changed, as far as remember.

> 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?

The values given at the end of g_energy run are wrong. You need to
use the g_analyses on the output of g_energy to get the right value.

> Thanks a lot for everybody in advance!
> 
> Jones
> 
> 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 ...
>>
>> XAvier
>>
>> >>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
>> gromacs?
>> >>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
>> of
>> >>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
>> values
>> >> > for every frame in your trajectory?
>> >> > I think the averages of mdrun -rerun are still incorrect, you need to
>> >>use
>> >> > the average of the values in the energy.xvg file.
>> >>
>> >>
>> >>  Ok, let me see if I understood: This means that, if I simulated
>> >>originally
>> >>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
>> divided
>> >>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
>> effects.
>> > 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
>> file
>> >>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
>> >g_analyze.
>> >
>> > 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
>> http://md.chem.rug.nl/~periole
>> -----------------------------------------------------
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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
http://md.chem.rug.nl/~periole
-----------------------------------------------------