Dear gromacs user, I have a system containing a solid surface(18000 atoms) and on top of it a heptapeptide solvated in water(SOL 9604), after a good minimisation and NVT equilibration and before production(which will be in NVT ensemble), I did NPT equilibration (1 bar) for 200 ps and continued to 1 ns as well, the average pressure results are coming below. ----------------------- pcoupl = Parrinello-Rahman Pcoupltype = isotropic ;;;;semiisotropic compressibility = 4.46e-5 ;;;;0.0 4.46e-5 ref_p = 1.0 ;;;1.0 1.0 tau_p = 2.0 refcoord-scaling = com ------------------------
Statistics over 100001 steps [ 0.0000 through 200.0000 ps ], 1 data sets All statistics are over 1001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure -782.581 39 925.396 -138.729 (bar) Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 1 data sets All statistics are over 5001 points Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure -746.168 18 921.982 3.41813 (bar) My first question as always is that if these amount of pressure and their RMSD together are satisfying the reference pressure of 1 bar that I considered? The second question: The water density I got is around 920 kg/m^3 in the middle of water region and far away from the solid surface, while I was expecting to get something around 997 kg/m^3 in the region far from the solid surface. And none of the tools like gmx inset-molecule, gmx solvate ... , does not let me add extra water molecule to the system, then, how I can increase the density of water in that region? Thanks in advance for your comments. Regards, Alex -- 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.