[gmx-users] Water molecules cannot be settled: V-rescale is the cause

Justin Lemkul jalemkul at vt.edu
Thu Sep 20 01:39:32 CEST 2012

On 9/19/12 5:10 PM, Ladasky wrote:
> After weeks of trying various conditions, I found my problem.  Here, from my
> position-restrained MDP file, are the two relevant lines:
> ; Temperature coupling is on
> tcoupl            = V-rescale ; Weak coupling for initial equilibration
> [snip]
> ; Pressure coupling is on
> pcoupl        = Berendsen     ; Pressure coupling on in NPT, also weak
> coupling
> This is a change that I forgot to mention in my list of changes, but in fact
> I did post the full MDP file.  I switched to using two DIFFERENT algorithms
> for temperature and pressure coupling when I performed the initial
> position-restrained equilibration.  This frequently sets up an INSTABILITY
> which manifests itself anywhere from a few picoseconds to a full nanosecond
> into the standard equilibrium MD run.

So the initial equilibration was NPT?  Did you ever try simply running NVT with 
either Berendsen or V-rescale before applying any type of pressure coupling? 
Immediate application of NPT is often unstable for a variety of reasons, not 
necessarily the temperature coupling algorithm.

> I am giving this number in real time, rather than in compute cycles, because
> I tried cutting my step time to 1.0 fs from my usual 2.0 fs -- and I still
> had a water molecule dislocate abruptly, at nearly the same physical
> location and simulated time point.
> I will share my full debugging process if anyone is interested.  It took me
> several runs, all of them over 24 hours long, to figure this out.
> Now, WHY would I have switched from a Berendsen temperature-coupling
> algorithm to the V-rescale algorithm?  Because of this cautionary note that
> I started receiving in GROMACS 4.5 when I started the position-restrained
> mdrun:
> NOTE 1 [file pr.mdp]:
>    The Berendsen thermostat does not generate the correct kinetic energy
>    distribution. You might want to consider using the V-rescale thermostat.
> I took this as a warning that a deeper study of the algorithms had revealed
> a flaw in Berendsen, and so I sought to use what GROMACS was advising me
> would be a better choice.  This is apparently MISLEADING advice when doing
> the initial equilibration.  If you are using the Berendsen pressure
> algorithm, you must also use the Berendsen temperature algorithm.
> I know that mdrun cannot be sophisticated enough to know which phase of my
> run I am performing, but I hope that the GROMACS documentation will be
> revised to discuss the appropriate use of the V-rescale thermostat.  I just
> misused it,and wasted a lot of time as a consequence.  I hope that some
> discussion of its proper use would be written and summarized on a page like,
> for example, this one:
> http://www.gromacs.org/Documentation/Terminology/Equilibration
> It already states: "Using, i.e., the Nosé-Hoover thermostat for initial NVT
> equilibration can lead to wild oscillations of the temperature, with the
> system ultimately blowing up."  A similar warning should be added about the
> V-rescale thermostat in NPT equilibration, ESPECIALLY if GROMACS is going to
> issue messages that recommend that you use it!
> There is a page for the Berendsen barostat/thermostat:
> http://www.gromacs.org/Documentation/Terminology/Berendsen
> There is apparently no corresponding page for the V-rescale thermostat.
> Perhaps one should be written.

Anyone is welcome to contribute to the wiki; it is a community project, after 
all.  I would also be interested to see if it can be demonstrated that NPT with 
V-rescale + Berendsen is unstable after an independent NVT simulation with 
either method.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list