[gmx-users] Error in Umbrella sampling

Justin Lemkul jalemkul at vt.edu
Tue Jun 24 12:07:22 CEST 2014

On 6/24/14, 2:57 AM, Maziya Ibrahim wrote:
> Hello all,
> I have been running the umbrella sampling tutorial available on the bevan
> lab website.
> After the following steps:
> grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt
> -o pull.tpr
> mdrun -s pull.tpr
> trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep
> When I run the distances.pl file  I get this error:
> "Fatal error:
> Molecule in topology has atom numbers below and above natoms (451).
> You are probably trying to use a trajectory which does not match the
> first 451 atoms of the run input file.
> You can make a matching run input file with tpbconv."
> I do not understand what changes to make to rectify this error. Any
> help is greatly appreciated.

That means you only have 451 atoms saved in traj.xtc and you're trying to write 
more atoms than that.  If you're doing the tutorial exactly, that shouldn't have 
happened because the simulations always save the whole system, but if you've 
used xtc-grps and only saved a subset of atoms, there's nothing that can really 
be done aside from what the fatal error tells you.  Of course, that's not really 
useful in trying to continue on to umbrella sampling, since you should keep the 
system the same composition throughout the windows.



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