[gmx-users] Solid state barostat

dgfd dgdfg roinato at mail.ru
Wed Mar 21 07:57:48 CET 2018

I am trying to simulate amorphous organic solid system with  Parrinello-Rahman at P=1 Bar. The maximal dt value which holds molecules together is 0.0008 and it's increasing leads to evaporation. What may be incorrect?
Berendsen works well with  dt=0.001 but it isn't recommended.
mdp options for pressure

Pcoupl          =       Parrinello-Rahman
tau_p           =       1.0
compressibility =       4.5e-05
ref_p           =       1

Water compressibility is used because the real is unknown and their densities are close.

May I asc one more question?
This system is a cubic box of N=1000 identical molecules. What is the most quick way to calculate pairwise distances between all molecules COM (1000x1000 matrix) in confout.gro file?
Now I am repeating 1000 times gmx distances command changing $i in selection file
resid $i plus resid 1;
resid $i plus resid 2;
resid $i plus resid 1000
May be exists the way of doing that in one step.

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