From: "Jones de Andrade" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@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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