Hello, I have looked in the manual and tried the adjustments for verlet-buffer-tolerance and rlist (with no sucess), but I did not find a plot for this? Can you direct me to this? I've copied my mdp below if anyone could give me some insight.
Thanks, Jo RUN PARAMETERS integrator = md tinit = 0 dt = 0.001 nsteps = 10000000 comm-mode = Linear nstcomm = 100 ;OUTPUT PARAMETERS nstlog = 50000 nstenergy = 10000 nstcalcenergy = 100 nstxout-compressed = 1000 compressed-x-precision = 1000 ; NEIGHBORLIST PARAMETERS cutoff-scheme = Verlet nstlist = 10 ns_type = grid pbc = xyz verlet-buffer-tolerance = 5.0e-6 ;-1 ; VDW AND COULOMB PARAMETERS coulombtype = PME rcoulomb = 0.9 coulomb-modifier = Potential-shift vdw-type = Cut-off rvdw = 0.9 vdw-modifier = Potential-shift table-extension = 1 ; EWALD PARAMETERS fourierspacing = 0.1 pme_order = 6 ewald_rtol = 1e-06 ewald_geometry = 3d epsilon_surface = 0 DispCorr = EnerPres ; BAROSTAT AND THERMOSTAT Tcoupl = no ;Nose-hoover Pcoupl = no ;Parrinello-Rahman refcoord-scaling = no ;SETUP VELOCITIES= gen_vel = no gen_temp = 298.15 gen_seed = -1 > > Message: 5 > Date: Mon, 12 Mar 2018 22:20:45 +0000 > From: Mark Abraham <mark.j.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] nve simulation > Message-ID: > <CAMNuMAQ-j7HN-Hz_UJ9CRKmirG=wbsMwSLQZT42_h=tui_mHUQ@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Hi, > > The list can't accept attachments. > > There's a plot in the reference manual that shows some indicative minimal > drifts, which would be a good place to search. :-) > > Mark > > On Mon, Mar 12, 2018 at 9:31 PM Jo <jojo412...@gmail.com> wrote: > > > Hello, > > > > I would like to run an NVE simulation but am having trouble conserving > the > > energy. From some past postings on the email list, I understand that > some > > neighborlist buffer parameters need to be adjusted, however I still am > not > > able to conserve energy. I am simulating a box of 1000 SPCE water, and I > > also suspect 'settles' could be causing the lack of energy conservation. > > Can anyone provide any suggestions on what I can do to conserve energy? > I > > have attached the mdp file. > > > > Thank you, > > > > Jo > > -- > > 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 167, Issue 53 > ****************************************************** > -- 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.