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

Xavier Periole X.Periole at rug.nl
Mon Aug 6 16:25:15 CEST 2007

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 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 
>> > 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 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 
> 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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