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 ?
Happy travellig through the Universe,
Niyaz
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