[gmx-users] NVT conserved-energy lysozyme
dommert at icp.uni-stuttgart.de
Tue May 15 12:53:23 CEST 2012
On Tue, 2012-05-15 at 09:17 +0100, David de Sancho wrote:
> Dear all
> I have been following Justin Lemkul's tutorial for the lysozyme
> I am using Gromacs 4.5.5.
Compiled in double or single precision ? If the latter one is the case,
perhaps numerical errors are the reason for the large energy drift.
> My concern is with the energy conservation in the implementation of
> Bussi's velocity-rescaling thermostat. In step 6 of the tutorial an
> NVT equilibration is run using tcoupl = V-rescale. The temperature
> equilibrates quite rapidly as shown in Justin's webpage. Essentially,
> T fluctuates around its equilibrium value after ~ 2 ps. However
> looking at the "conserved energy" I find that there is a drift that
> does not seem to plateau even by the end of the 100 ps run (see
> I have tried to sort this out myself by using the following settings:
> (1) change lincs_iter from 1 to 2.
> (2) change from PME to PME-Switch, which for NVE Gromacs recommends as
> more accurate (I also modified: rlist=1.0, rcoulomb=1.0, rvdw=1.4).
> (3) change to vdwtype = Shift, so that errors due to cutoffs were
> None of this seems to help.
> Actually Justin himself has helped me and found that with the
> following settings the conservation is considerably better
> === shift settings ===
> vdwtype = shift
> coulombtype = PME
> rlist = 1.4
> rcoulomb = 1.4
> rvdw = 1.0
> rvdw_switch = 0.8
> Still there is a drift in the "conserved quantity" which seems a quite
> severe problem.
> Can anyone give some pointers on how to sort this out?
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Dipl. - Phys.
Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658
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