[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem
gozde ergin
gozdeeergin at gmail.com
Thu Nov 5 13:23:30 CET 2015
- system 512 water molecule covered by 25 organic on each surface,
- I used both gromacs 4.5 and 5.0 with and without double precision
- .mdp file is :
integrator = md
dt = 0.002
nsteps = 10000000 ; 20 ns
nstxout = 10000
nstvout = 10000
nstlog = 10000
nstenergy = 10000
continuation = 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-hoover
tc-grps = System
tau_t = 1.0
ref_t = 300
Pcoupl = No
pbc = xyz
DispCorr = EnerPres
gen_vel = yes
gen_temp = 310
gen_seed = -1
nstcomm = 10
comm-mode = Linear
comm-grps = System
hope it is readable now!
best
On Thu, Nov 5, 2015 at 11:44 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> 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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> > >
> > >
> > > --
> > > Best Regards,
> > > Ganesh Shahane
> > > --
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