[gmx-users] Dr.Lemkul's Umbrella Sampling Tutorial - grompp note on leap frog/Nose-Hoover

Justin Lemkul jalemkul at vt.edu
Tue Nov 4 01:48:20 CET 2014

On 11/3/14 7:37 PM, Agnivo Gosai wrote:
> Dear Users
> I am following the Umbrella Sampling tutorial by Dr. Lemkul. I am using
> GROMACS version 4.5.6.
> In step 6 of the tutorial where the umbrella sampling simulations are done
> for each of the extracted configurations based on COM distance sampling
> from 0.5 - 5.0 nm along z axis , I have 27 sets.
> For each set I need to do a short NPT equilibration and an Umbrella run.
> While running "grompp" for the 1st configuration before the NPT
> equilibration the terminal showed the following message :
> NOTE 1 [file md_umbrella.mdp]:
>    leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
> My question is how will this affect my simulations ?

It's an innocuous message.  There are inherent limitations in compatibility of 
various algorithms and options.  Notes are simply FYI.  Warnings and errors 
indicate problems.



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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