> > Message: 3 > Date: Tue, 11 Jul 2017 12:57:05 -0400 > From: Justin Lemkul <jalem...@vt.edu> > > Moreover, I observed that this time I got lower values for P during the NPT > > equilibration, but still is too far from 1 bar. I really don't understand > > why for the NVT simulation I get a T around 298, but as soon as I turn on > > the pcoupl, the T rises to 300-301 K and the P gets average values of 7 > > and 4 bar (vs 8 and 14 for the previous simulations). Then at the end of > > the 1-ns MD the temperature remains around 301 and the P is -1 and 2.7 > > bar. Considering the parameters I am using, is there anything I can change > > to make the P coupling better? I am running a 3 nm box with 308 molecules. > > This is the full mdp file: > > > > http://www.gromacs.org/Documentation/Terminology/Pressure > > Your box is very small and will be subject to large fluctuations.
Dear Justin, I increased the size of the simulation box to 4 nm. Indeed, the values of pressure improved (averages around -1 bar or 1.5, 2 bar, or so). However, the T keeps being overestimated (302 K). During NVT I got the right value, so I decided to run the 200 ns NPT equilibration with Berendsen barostat instead of P-R. I got the right T value, around 298.3 and a pressure of 1.5 more or less. Then I launched a continuation test with 200 ps MD with P-R (I couldn't use the -e option because it gives me the error Could not find energy term named 'Box-Vel-XX', moreover, I didn't use P-R before so I guess I shouldn't expect stored values for it?. But I am using -t ). Despite I got low pressure averages around 0.5 bar, the temperature raised again to 301-302. This happens very early in the simulation, which seems to indicate that for sd integrator/thermostat and P-R barostat there is something going on. I am getting practically the same density in between simulation, so I guess I can say tha t in term of P, the system has been equilibrated. However, what can I do to get the right T for this system? If I was able to get the right T with Berendsen barostat, I don't understand what's wrong when I change to P-R. Thank you in advance, Sonia Aguilera PhD student ENSCM > > -Justin > > > ; Run control > > integrator = sd ; Langevin dynamics > > tinit = 0 > > dt = 0.0005 > > nsteps = 2000000 ; 1 ns > > nstcomm = 100 > > ;energygrps = non-Water > > ; Neighborsearching and short-range nonbonded interactions > > cutoff-scheme = verlet > > nstlist = 20 > > ns_type = grid > > pbc = xyz > > rlist = 1.2 > > ; Electrostatics > > coulombtype = PME > > rcoulomb = 1.2 > > ; van der Waals > > vdwtype = cutoff > > vdw-modifier = force-switch > > rvdw-switch = 1.0 > > rvdw = 1.2 > > ; Apply long range dispersion corrections for Energy and Pressure > > DispCorr = no > > ; Spacing for the PME/PPPM FFT grid > > fourierspacing = 0.12 > > ; EWALD/PME/PPPM parameters > > pme_order = 6 > > ewald_rtol = 1e-06 > > epsilon_surface = 0 > > ; Temperature coupling > > ; tcoupl is implicitly handled by the sd integrator > > tc_grps = system > > tau_t = 1.0 > > ref_t = 298.15 > > ; Pressure coupling is on for NPT > > Pcoupl = Parrinello-Rahman > > tau_p = 1.0 > > compressibility = 4.5e-05 > > ref_p = 1.0 > > ; Do not generate velocities > > gen_vel = no > > ; options for bonds > > constraints = none ; we only have C-H bonds here > > ; Type of constraint algorithm > > constraint-algorithm = lincs > > ; Constrain the starting configuration > > ; since we are continuing from NPT > > continuation = yes > > ; Highest order in the expansion of the constraint coupling matrix > > lincs-order = 12 > > > > > > Thank you very much, > > > > Sonia Aguilera > > PhD student > > ENSCM > >> ; Run control > >> integrator = sd ; Langevin dynamics > >> tinit = 0 > >> dt = 0.0005 > >> nsteps = 40000000 ; 20 ns > >> nstcomm = 100 > >> ; Neighborsearching and short-range nonbonded interactions > >> cutoff-scheme = verlet > >> nstlist = 20 > >> ns_type = grid > >> pbc = xyz > >> rlist = 1.2 > >> ; Electrostatics > >> coulombtype = PME > >> rcoulomb = 1.2 > >> ; van der Waals > >> vdwtype = cutoff > >> vdw-modifier = potential-switch > >> rvdw-switch = 1.0 > >> rvdw = 1.2 > >> ; Apply long range dispersion corrections for Energy and Pressure > >> DispCorr = EnerPres > > > > CHARMM uses a force switch, and only apply dispersion correction in the > > case of > > lipid monolayers. > > > > http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM > > > > -Justin > > > > ================================================== > > > > -- > ================================================== -- 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.