[gmx-developers] Disparity in total energy between consecutive steps

[Mark Abraham]

Hi,

This would be a good question for the user's mailing list, since it doesn't
pertain to the code development. Please continue there.

I suggest you look at the change in energy when you release position
restraints after a run that wasn't heated. Why shouldn't there be a drop in
energy when you change the Hamiltonian?

Mark

On Thu, 1 Jun 2017 23:19 Felix Y Yang <fyy001 at ucsd.edu> wrote:

> Hi all,
>
>
> So I've been trying a series of runs of heating-active-site-of-protein,
> then NVE, then heating again, and NVE again. And I've seemed to notice that
> the total energy of the system between the end of the heating process and
> the beginning of a NVE step right after it is significantly different,
> namely dropping a lot in total energy. The total energy seems to be
> retained a lot better between the end of an NVE step and the beginning of
> the next heating step.
>
>
> Does anyone know what might be the cause of this? I have the protein
> position-restrained during the heating step, and released during the NVE
> step. The heating step is 3 ps, the NVE is 1 ns. For the heating step, I
> grouped the active site of the protein separately in an index file, and
> heated only that group, while the rest of the protein has the thermostat
> turned off. The other parameters in my mdp file are almost exactly the same
> for the heating and NVE processes.
>
>
> Any feedback would be appreciated.
>
>
> Thanks,
>
>
> Felix Yang
>
> Graduate Master's Student
> Department of Chemistry & Biochemistry
> University of California, San Diego
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20170601/b45bf716/attachment-0002.html>