[gmx-users] gromacs.org_gmx-users Digest, Vol 167, Issue 53

[Mark Abraham]

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 <jojo412202 at 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.abraham at gmail.com>
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] nve simulation
> > Message-ID:
> >         <CAMNuMAQ-j7HN-Hz_UJ9CRKmirG=wbsMwSLQZT42_h=tui_mHUQ at 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 <jojo412202 at 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
> > > --
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