Hi, Please don't reply to digests. Please don't subscribe to digests if you actually want to post and discuss :-)
See figure 3.5, or search for "drift" ;-) Mark On Tue, Mar 13, 2018 at 6:28 PM Jo <jojo412...@gmail.com> wrote: > 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. > -- 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.