[gmx-users] NVT conserved-energy lysozyme

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 15 12:49:34 CEST 2012

On 15/05/2012 6:17 PM, David de Sancho wrote:
> Dear all
> I have been following Justin Lemkul's tutorial for the lysozyme 
> simulations
> http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html
> I am using Gromacs 4.5.5.
> My concern is with the energy conservation in the implementation of 
> Bussi's velocity-rescaling thermostat.

Check out their paper and see what they claim for conservation properties.

>  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).

Different observables equilibrate over different time scales.

> 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 
> eliminated.
> 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.

"Severe" sounds like an over-description. The drift is 0.15% in the 
conserved quantity, beginning from a non-equilibrated starting point and 
only continuing for about the shortest equilibration period anybody 
could imagine using these days. There's a lot of approximations going on 
(PME, rigid bonds, static point charges) and maybe drift at this level 
is not significant. Still, it should get smaller if you just run for longer.

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