On Mon, Feb 18, 2013 at 5:24 AM, Wui Zhuan Lim <wuizhu...@hotmail.com>wrote:
> > Hi all, > > I'm a beginner in using Gromacs and MD simulation works. > I am currently doing a simulation of enzyme unfolding. > When I began NVT equilibration, a warning note appeared, as shown below: > With twin range cut-offs and SHAKE the virial and pressure are incorrect. > At first, I tried to ignore the warning with -maxwarn (although it's > better not to use it, just have a try) > The warning did disappear. > As > I move forward to NPT, the same message appeared again. But it's no > longer "warning", but "error" instead, which cannot be avoided with > -maxwarn, so I could not proceed NPT at the moment. > So I was > wondering if it's a serious issue to fix it. I understand what twin > range cut-offs and SHAKE are, but how will I know the appropriate virial > and pressure? > If a combination of algorithms isn't implemented and there's an error that prevents it, then the GROMACS authors were serious about it :-) What GROMACS version is this? Why are you using SHAKE rather than LINCS? Also note that your PME parameters are very crude, and that re-generating velocities when you start NPT is generally not what you want to do. Mark > > Regards, > Adam > > **Below are my mdp files for NVT and NPT: > > NVT > > title = Protein-ligand complex NVT equilibration > define = -DPOSRES > ; Run parameters > integrator = sd > nsteps = 10000 > dt = 0.002 > ; Output control > nstxout = 100 > nstvout = 100 > nstenergy = 100 > nstlog = 100 > energygrps = Protein Non-Protein > ; Bond parameters > continuation = no > constraint_algorithm = shake > constraints = hbonds > ; Neighborsearching > ns_type = grid > nstlist = 5 > rlist = 0.9 > rcoulomb = 0.9 > rvdw = 1.4 > ; Electrostatics > coulombtype = PME > pme_order = 3 > fourierspacing = 0.16 > ; Temperature coupling > tc_grps = Protein Water_and_ions > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Pressure coupling > pcoupl = no > ; Periodic boundary conditions > pbc = xyz > ; Dispersion correction > DispCorr = EnerPres > ; Velocity generation > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > > > > NPT > > title = Protein-ligand complex NVT equilibration > define = -DPOSRES > ; Run parameters > integrator = sd > ld_seed = -1 > nsteps = 2500000 > dt = 0.002 ; 2 fs > ; Output control > nstxout = 100 > nstvout = 100 > nstenergy = 100 > nstlog = 100 > energygrps = Protein Non-Protein > ; Bond parameters > continuation = no > constraint_algorithm = shake > constraints = hbonds > shake_tol = 0.0000001 > ; Neighborsearching > ns_type = grid > nstlist = 5 > rlist = 0.9 > rcoulomb = 0.9 > rvdw = 1.4 > ; Electrostatics > coulombtype = PME > pme_order = 3 > fourierspacing = 0.16 > ; Temperature coupling > tc_grps = Protein Water_and_ions > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Pressure coupling > pcoupl = Berendsen > pcoupltype = isotropic > tau_p = 2.0 > ref_p = 1.0 > compressibility = 4.5e-5 > refcoord_scaling = com > ; Periodic boundary conditions > pbc = xyz > ; Dispersion correction > DispCorr = EnerPres > ; Velocity generation > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
