[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem
Mark Abraham
mark.j.abraham at gmail.com
Thu Nov 5 11:45:03 CET 2015
Hi,
You're making it very hard to help you, by not providing a readable .mdp
file, not specifying a GROMACS version, nor describing what is in your
system. If there was a magic "do this and energy is conserved" button then
it'd be already pushed for you ;-)
Mark
On Thu, Nov 5, 2015 at 11:34 AM gozde ergin <gozdeeergin at gmail.com> wrote:
> Hi Ganesh
>
> I tried your suggestion and this time instead of decreasing, potential and
> kinetic energy kept increasing!
> So still could not get the converged-constant energy for NVE.
>
>
> On Wed, Nov 4, 2015 at 4:23 PM, Ganesh Shahane <ganesh7shahane at gmail.com>
> wrote:
>
> > Hi Gozde,
> >
> > You could try modifying and introduce some of the parameters as follows
> > (keeping the rest same) -
> >
> > lincs_iter = 2
> > rvdw-switch = 1.1
> > vdwtype = Cut-off
> > vdw-modifier = Force-switch
> >
> > I recently faced some of the same problems as yours and the above
> > parameters worked for me.
> >
> > On Wed, Nov 4, 2015 at 2:47 PM, gozde ergin <gozdeeergin at gmail.com>
> wrote:
> >
> > > Dear Chaban,
> > >
> > > I decreased the time step and also I run by using double precision
> > however
> > > energy kept decreasing and did not converge.
> > >
> > > Does anybody has an opinion how to run NVE simulation in Gromacs
> without
> > > energy drifting?
> > >
> > > Bests
> > >
> > >
> > > On Tue, Nov 3, 2015 at 7:27 PM, Vitaly V. Chaban <vvchaban at gmail.com>
> > > wrote:
> > >
> > > > Decrease the time-step.
> > > >
> > > >
> > > >
> > > >
> > > > On Tue, Nov 3, 2015 at 3:00 PM, gozde ergin <gozdeeergin at gmail.com>
> > > wrote:
> > > >
> > > > > ---------- Forwarded message ----------
> > > > > From: gozde ergin <gozdeeergin at gmail.com>
> > > > > Date: Tue, Nov 3, 2015 at 5:39 PM
> > > > > Subject: NVT to NVE ensemble, energy drifting problem
> > > > > To: mailing list Gromacs <
> gromacs.org_gmx-users at maillist.sys.kth.se>
> > > > >
> > > > >
> > > > > Dear Gromacs user,
> > > > >
> > > > > I did some simulation in NVT ensemble now I need to switch and do
> > some
> > > > more
> > > > > simulations in NVE ensemble.
> > > > > What properties do I need to change in .mdp file to get a good
> energy
> > > > > conversion?
> > > > > I used the same properties like NVT without temperature coupling
> but
> > my
> > > > > potential and kinetic energy drifted a lot.
> > > > > What should I do prevent this drifting?
> > > > >
> > > > > Here is my nvt.mdp:
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > *integrator = md dt =
> > > > > 0.002nsteps = 10000000 ; 20 nsnstxout
> > > > > = 10000nstvout = 10000nstlog =
> > > > > 10000nstenergy = 10000continuation = no
> > > > > constraint_algorithm = lincs constraints = all-bonds
> > > > > lincs_iter = 1 lincs_order = 4
> > ns_type
> > > > > = grid nstlist = 5 rlist =
> > > > > 1.2 rcoulomb = 1.2 rvdw =
> > > > > 1.2 coulombtype = PME pme_order =
> > > > > 4 fourierspacing = 0.16 tcoupl
> > =
> > > > > nose-hoovertc-grps = Systemtau_t
> > =
> > > > > 1.0ref_t = 300Pcoupl = Nopbc
> > =
> > > > > xyz DispCorr = EnerPres gen_vel =
> > > > > yes gen_temp = 310 gen_seed =
> > > > > -1 nstcomm = 10comm-mode =
> > > > > Linearcomm-grps = System *
> > > > > For nve, I just make the temperature coupling off and used the same
> > > > > properties however as I mentioned my energy could not converged in
> 20
> > > ns.
> > > > >
> > > > > Thanks in advance
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
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> > > > --
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> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
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> >
> >
> >
> > --
> > Best Regards,
> > Ganesh Shahane
> > --
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