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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_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-users or send a mail to gmx-users-requ...@gromacs.org.
