Hi Niyaz,
The author of the package will have the best answers to these questions.
But you should be able to find in the source files where the mdp file is
written. There you can make changes, to make sure that coulombtype is set
to PME and tcoupltype is set to v-rescale. In addition, you probably want
to set nstxtcout to some value to get an XTC file.
To find the file(s) where the mdp stuff is handled, you can go to the
directory with the source code and run
find -name "*.py" -exec grep mdp {} \; -print
That will find .py files, grep each file found for mdp and print the
filename if it was found.
Hope it helps,
Tsjerk
On Sep 13, 2014 6:16 AM, "N. S." <niyaz.sa...@gmail.com> wrote:
> Dear, PyMol-Gromacs experts,
>
> I used to use PyMol Dynamics plugin to make some MDs.
> It makes me more than sad I always get notes like:
> ---------------------------------
> NOTE 1 [file em.mdp]:
> You are using a plain Coulomb cut-off, which might produce artifacts.
> You might want to consider using PME electrostatics.
>
> NOTE 2 [file pr.mdp]:
> The Berendsen thermostat does not generate the correct kinetic energy
> distribution. You might want to consider using the V-rescale thermostat.
> ---------------------------------
> Does anybody know how do I adjust config.files to make default PME
> and V-rescale thermostat ? And where are the corresponding files, please ?
>
> And, I am sory, another quest., How do I make the plugin produce .xtc
> tarajectory files instead of trr, tpr.., by default ?
>
> Thank you in advance,
>
> Happy journay through the Universe,
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
