[gmx-users] error in umbralla sampling step 6

Justin Lemkul jalemkul at vt.edu
Sat Oct 26 17:18:02 CEST 2013

On 10/26/13 10:45 AM, sunyeping wrote:
> Dear gromacs user,
> I am doing umbralla sampling on a protein-ligand system following the gromacs umbralla sampling turial. It seems that the first five steps go well, and I select 23 gro files as the starting configurations of adjacent umbrella sampling windows. However when I use grompp to generate tpr files for these individual configurations as following:
> grompp -f npt_umbrella.mdp -c conf86.gro -p topol.top -n index.ndx -o npt86.tprI get the following notes, warning and error information:NOTE 1 [file npt_umbrella.mdp]:
>    nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
>    nstcomm to nstcalcenergy
> NOTE 2 [file npt_umbrella.mdp]:
>    leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1

The notes are harmless.

> 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.

You should not use Nose-Hoover for your initial equilibration.  Heed what grompp 

> ...............Largest charge group radii for Van der Waals: 16.306, 16.297 nm
> Largest charge group radii for Coulomb:       16.306, 16.297 nm
> WARNING 2 [file npt_umbrella.mdp]:
>    The sum of the two largest charge group radii (32.603355) is larger than
>    rlist (1.400000)
> ....................Fatal error:
> Too many warnings (2), grompp terminated.
> If you are sure all warnings are harmless, use the -maxwarn option.
> Discussion
>   aout warring 2 on the mail-list points out that the error that cause
> warning 2 will impact the results and lead to artifacts. I cann't
> understand why the warning occurs here, because it didn't appear when I
> use grompp in the my previous steps.  Could you explain why it occur in this step? Will it really affect umbralla sampling? Can I use the -maxwarn option to ignore it?

Given the size of the cited charge group radii, you probably have a molecule 
broken across PBC, which is not a real issue.  trjconv -pbc mol or -pbc whole 
would confirm.  If trjconv processing causes the error to go away, that's all it 



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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