[gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

gozde ergin gozdeeergin at gmail.com
Fri Nov 6 10:32:06 CET 2015


Hi Mark,

As your suggestion I used cutoff sheme = Verlet with running in Gromacs 5.1
Now instead of decreasing, total energy kept increasing! Do you think this
behavior is normal?

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Kinetic En.                 8537.49        180    386.122    1253.25
(kJ/mol)
Potential                  -20741.9        530    1092.62    3652.89
(kJ/mol)
Total Energy               -12204.4        710    1449.39    4906.14
(kJ/mol)
Temperature                 319.933        6.7    14.4695    46.9643  (K)


Thanks in advance.


On Thu, Nov 5, 2015 at 2:15 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> So that means you are using the group cutoff scheme without a cutoff
> buffer, which is known not to conserve energy (see manual sections on
> neighbour searching). You can either choose a group-scheme model physics
> where the buffer (set with rlist) is suitably larger than the cutoffs
> (which is awkward to set up and will run slowly), or use the Verlet scheme
> (which has a buffer by default and runs fast) which is now default in 5.1.
> Even with that fixed, the use of constraints intrinsically leads to drift,
> also. Whether the remaining drift matters for your simulation (vs the
> decrease in sampling you would have to accept in order to start to deal
> with it) is an open research question.
>
> Mark
>
>
> On Thu, Nov 5, 2015 at 1:23 PM gozde ergin <gozdeeergin at gmail.com> wrote:
>
> > - 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
> > > > > > > > --
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> > > > > > --
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> > > > > --
> > > > > Best Regards,
> > > > > Ganesh Shahane
> > > > > --
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