Dear Erik, Thank you very much for helping me. I have got 2 errors from grompp using gromacs v5.1.
ERROR 1 [file nve.mdp]: With Verlet lists only full pbc or pbc=xy with walls is supported ERROR 2 [file nve.mdp]: With Verlet lists nstlist should be larger than 0 How can I fix these? I copied my mdp file. ############################################# title = NVE equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 100000000 ; 1 * 100000000 fs= 100000 ps = 100 ns dt = 0.001 ; 1 fs ; mode for center of mass motion removal comm-mode = Angular ; Output control nstxout = 5000 nstvout = 5000 nstenergy = 5000 nstlog = 500 ;energygrps = ; Bond parameters continuation = no constraint_algorithm = lincs constraints = hbonds lincs_iter = 2 lincs_order = 4 ; Neighborsearching PARAMETERS vdw-type = cut-off verlet-buffer-tolerance = -1 rlist = 1 nstlist = 0 ns_type = grid pbc = no ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = cut-off rcoulomb-switch = 0 rcoulomb = 0.0 rvdw = 0.0 rvdw-switch = 0.0 fourierspacing = 0.16 epsilon_r = 1 epsilon_rf = 78 ; EWALD/PME/PPPM parameters pme_order = 4 ; cubic interpolation ; Temperature coupling tcoupl = no ;tc-grps = ;tau_t = 0.1 ;ref_t = 300 ; Pressure coupling pcoupl = no ; no pressure coupling in NVT ; Dispersion correction ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ################################################################ Best regards, Mijiddorj > ------------------------------ > > > > Message: 4 > > Date: Fri, 20 Jan 2017 10:30:59 +0000 > > From: Erik Marklund <erik.markl...@kemi.uu.se> > > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > > Subject: Re: [gmx-users] Simulation in vacuum > > Message-ID: <7745284c-ea36-4189-80a6-0a6ab4986...@kemi.uu.se> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Mijiddorj, > > > > We have had good energy conservation with bond constraints and a 1 fs > time > > step under double precision, using a setup similar to yours. We did not > > remove rotation however, because we wanted to honour the rotational > > temperature of the system. Whether that is an important choice or not is > > for you to decide, but do note that the spinning ice cube effect is an > > artefact arising from the thermostat, which is turned off in your setup. > > > > Whether bonds should be constrained or not is related to what your > > scientific questions are, and the time step depends on what bonds are > > constrained, if any. I can?t remember what LINCS parameters we used, but > be > > prepared to increase the order and/or iter. Consult the manual for > details. > > > > Kind regards, > > Erik > > > > ______________________________ > > Erik Marklund, PhD > > Marie Sk?odowska Curie INCA Fellow > > Department of Chemistry ? BMC > > Uppsala Universtity > > erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> > > > > On 20 Jan 2017, at 11:01, ????? ????????? <b.mijidd...@gmail.com<mailto: > > b.mijidd...@gmail.com>> wrote: > > > > Dear gmx users, > > > > I would like to get experience of simulation in vacuum. Please suggest me > > tutorials, and advice me. > > > > I read about following comments which written on Shourjiya Sanyal > tutorial. > > Can you discuss about it? > > > > In vacuum simulation, integration should be reduced compared to solvent > > phase simulation. Periodic boundary conditions, non-bonded interaction > > cutoffs, temperature coupling and pressure coupling were all turned off. > > Center of mass translation and rotation around the center of mass are to > be > > removed to avoid the fast spin of the protein. One should also constrain > > the hydrogen bond using algorithms like SHAKE/LINCS. > > > > http://www.shourjya.thinkbiosolution.com/md- > simulation-in-gas-phasevacuum- > > with-gromacs/ > > > > > > Best regards, > > Mijiddorj > > -- > > 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. > > > > > > ------------------------------ > > > > -- > > 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. > > > > End of gromacs.org_gmx-users Digest, Vol 153, Issue 91 > > ****************************************************** > > > > > ------------------------------ > > -- > 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. > > End of gromacs.org_gmx-users Digest, Vol 153, Issue 93 > ****************************************************** > -- 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.