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
says.
...............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
was.
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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