[gmx-users] Fattal error in npt_umbrella : Umbrella Sampling Simulations tutorial

Justin Lemkul jalemkul at vt.edu
Sat Feb 6 00:38:06 CET 2016

On 2/5/16 2:50 PM, Alexander Alexander wrote:
> Dear Gromacs user,
> I am trying to do the Umbrella simulation following exactly the the
> tutorial, everything is fine but I a fatal error happens in .tpr file
> generation of npt_umbrella section warning about Pcoupl in npt_umbrella.mdp
> file.
> I used the suggested .mdp file in tutorial with Parrinello-Rahman pressure
> coupling, but it complained that this type of coupling make the
> equilibration unstable, and use Berendsen pressure coupling instead.
> Then, I did, but again Fatal error by an warning stating that Berendsen
> invalidates the true ensemble for the thermostat.

Use of the Berendsen weak coupling should not trigger a fatal error.  It should 
produce a note for the user.  Can you provide the exact output from the screen, 
copied and pasted?

> All the inputs and even the name are fully identical with the tutorial
> samples.
> The version of Gromacs is : VERSION 5.1-rc1

Don't use release candidates for production work :)  Get the newest version (5.1.2).



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


More information about the gromacs.org_gmx-users mailing list