[gmx-users] NVT conserved-energy lysozyme

David de Sancho daviddesancho at gmail.com
Tue May 15 10:17:23 CEST 2012

Dear all
I have been following Justin Lemkul's tutorial for the lysozyme simulations
I am using Gromacs 4.5.5.

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 attachment).

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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