Hi, I am trying to simulate a short protein (160aa) in water and after 500ps NPT equilibration I got rather high value for density: average is 1014 and pretty stable around this value, but quite noisy (peaks 1010-1020). Also the pressure is very noisy with average about -7 (I am not sure it is that bad since the fluctuations there are really big).
I used the AMBER03 FF with these settings for temperature and pressure coupling: ; Temperature Coupling tcoupl = V-rescale tc_grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Pressure Coupling pcoupl = parrinello-rahman pcoupltype = isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com Previously made 100ps NVT equilibration (with modified Berendsen) gave stable and quiet 300K. What might be a problem here (if any)? Would it be better if I used Nose-Hoover thermostat for temperature coupling (I suppose no as they both are expected to give corrected ensembles)? Thank you. -- View this message in context: http://gromacs.5086.n6.nabble.com/High-density-after-NPT-tp5003950.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
