Hi, You're using quite an old version of GROMACS, which unfortunately means the warning message issued by GROMACS 2018 and more recent is not available to you ( http://manual.gromacs.org/documentation/2018/release-notes/miscellaneous.html#added-grompp-note-for-parrinello-rahman-position-restraints). That suggests Berendsen pressure coupling in such cases, because position restraints within a box whose volume changes is not an intrinsically well defined model. Asking your compute center for a more recent GROMACS version will probably run faster and have fewer bugs, too ;-)
Mark On Tue, 18 Jun 2019 at 12:18, Patricia Saenz Méndez <[email protected]> wrote: > Hi! > I am trying to run a simulation of a membrane protein (without the > membrane), and to this end I am trying to fix the region of the protein > that is inserted in the hydrophobic part of the membrane. It is not a > transmembrane protein, just an helix is"touching" the lipophylic part of > the membrane. > I used genrestr and an index file. I could equilibrate the system. But when > trying to run the actual MD simulation (200 ns) I just get the calculation > finished in a couple of minutes and apparently just run 100 ps (like during > equilibration). > There it goes the command line (gromacs 5.1): > > mpirun -np 200 gmx_mpi grompp -f md_NPT_200ns.mdp -c 1w6j-wild_npt.gro -t > 1w6j-wild_npt.cpt -p 1w6j-wild.top -n index.ndx -o 1w6j-wild_md_200ns.tpr > > mpirun -np 200 gmx_mpi mdrun -s 1w6j-wild_npt.tpr -deffnm > 1w6j-wild_md_200ns > > and the mdp file: > > define = -DPOSRES_MEMBRANE ; position restrain the membrane region > ; Run parameters > integrator = md ; leap-frog integrator > nsteps = 100000000 ; 2 * 100000000 = 200000 ps (200 ns) > dt = 0.002 ; 2 fs > ; Output control > nstxout = 5000000 ; save coordinates every 100.0 ps > nstvout = 5000000 ; save coordinates every 100.0 ps > nstenergy = 2500 ; save energies every 5.0 ps > nstlog = 25000 ; update log file every 50.0 ps > nstxtcout = 2500 ; write .xtc trajectory every 5.0 ps > energygrps = Protein > ; Bond parameters > continuation = yes ; first dynamics run > constraint_algorithm = lincs ; holonomic constraints > constraints = all-bonds ; all bonds (even heavy atom-H bonds) > constrained > lincs_iter = 1 ; accuracy of LINCS > lincs_order = 4 ; also related to accuracy > ; Neighborsearching > cutoff-scheme = Verlet > ns_type = grid ; search neighboring grid cells > nstlist = 5 ; 10 fs, largely irrelevant with Verlet > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) > rvdw = 1.0 ; short-range van der Waals cutoff (in nm) > ; Electrostatics > coulombtype = PME ; Particle Mesh Ewald for long-range > electrostatics > pme_order = 4 ; cubic interpolation > fourierspacing = 0.16 ; grid spacing for FFT > ; Temperature coupling > tcoupl = V-rescale ; modified Berendsen thermostat > tc-grps = Protein Non-Protein ; two coupling groups - more accurate > tau_t = 0.1 0.1 ; time constant, in ps > ref_t = 300 300 ; reference temperature, one > for each group, in K > ; Pressure coupling > pcoupl = Parrinello-Rahman ; pressure coupling is on for > NPT > pcoupltype = isotropic ; uniform scaling of box > vectors > tau_p = 2.0 ; time constant, in ps > ref_p = 1.0 ; reference pressure, in bar > compressibility = 4.5e-5 ; isothermal compressibility of > water, bar^-1 > ; Periodic boundary conditions > pbc = xyz ; 3-D PBC > ; Dispersion correction > DispCorr = EnerPres ; account for cut-off vdW scheme > ; Velocity generation > gen_vel = no ; assign velocities from Maxwell distribution > > > What am I doing wrong? > Thanks in advance, > > P > -- > 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 [email protected]. > -- 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 [email protected].
