[gmx-users] Umbrella Sampling gromacs 5.0 error

Alexander Law alexander.law at pg.canterbury.ac.nz
Mon Nov 24 04:29:59 CET 2014

The npt_umbrella.mdp which reads continuation = yes, gen-vel = yes, is located at the first link I provided, within the compressed folder. Not from the link in your tutorial.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Monday, November 24, 2014 1:47 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Umbrella Sampling gromacs 5.0 error

On 11/23/14 3:56 PM, Alexander Law wrote:
> Hi Justin
> I downloaded the compressed folder from this website: http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Computing_potentials_of_mean_force%3A_Justin_Lemkul,_Session_2A
> Within it the the npt_umbrella.mdp file reads continuation = yes, gen-vel = yes.
> I've ran ~15 simulations over the weekend with continuation = yes, gen-vel= no
> Are these simulations unsuitable for umbrella sampling?

The settings should be somewhat intuitive; if you are continuing a run (i.e.
some previous time interval or from equilibration), you should not generate
velocities (continuation = yes, gen_vel = no).  If you are starting a new
simulation, i.e. equilibration (continuation = no) then you should generate
velocities (gen_vel = yes).

I have checked twice since you originally posted this problem, and
npt_umbrella.mdp provided with the tutorial (for equilibration) is correct
(continuation = no, gen_vel = yes) and the input for umbrella sampling
(md_umbrella.mdp) is also correct (continuation = yes, gen_vel = no), so I don't
know what this issue related to the contents of npt_umbrella.mdp is.

> ---------------------------
> I am assuming they are, so I've started a new sequence with not_umbrella.mdp reading the same as: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp
> This produces this error:
>   WARNING 1 [file npt_umbrella.mdp]:
>    You are generating velocities so I am assuming you are equilibrating a
>    system. You are using Parrinello-Rahman pressure coupling, but this can
>    be unstable for equilibration. If your system crashes, try equilibrating
>    first with Berendsen pressure coupling. If you are not equilibrating the
>    system, you can probably ignore this warning.
> Since I am not equilibrating I've avoided this using the -maxwarn command and started a new sequence for umbrella sampling.

Again, npt_umbrella.mdp *is* intended for equilibration; the warning probably
shouldn't be a fatal one for grompp, but it is indicating that instability may
result.  If the simulations proceed, that's fine.  The warning should probably
just be a note, instead, but in general one should not generate velocities with
Nose-Hoover, which allows for wider fluctuations than a weak coupling method
like Berendsen or V-rescale, which are more robust for equilibration.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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