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

Jones de Andrade johannesrs at gmail.com
Mon Aug 6 16:13:44 CEST 2007

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?

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?

Also obtaining accurate potential energy averages for even small systems
> requires a LOT of statistics.

I know it. It's just the first runs (only 200k steps of simulation, 20k
steps saved), and the results will guide me towards the proper acquisition
time.  ;)

Thanks a lot you both for the help in advance.

Sincerally yours,

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