[gmx-users] tutorial umbrella sampling

Justin Lemkul jalemkul at vt.edu
Sun Nov 29 07:04:22 CET 2015

On 11/27/15 5:36 PM, Matthias Kiesel wrote:
> Hi All,
> I am currently doing the umbrella sampling tutorial by Justin Lemkul, but i have
> a problem with creating the right configurations for the umbrella sampling run.
> After running the first pull simulation and the given perl script the com
> distances don´t go from 0.5nm to 5nm, instead they start at 0nm, go negative for
> a some time grow until ~0.3nm and go back to small and negative values again.

That's definitely not right.  Visualize the trajectory - does this match the 
behavior there?  The pull should be pretty straightforward.

> When I visualize some of the .gro files (like conf250.gro) I can see something
> being pulled away from the rest of the Protein (how can I verify its Chain_A?)

It's the first peptide, numerically, and you created an index group for it in a 
prior step in the tutorial.

> and in the created pullx.xvg the desired a COM-Distance curve going from 0.5nm
> to ~5nm is shown. Thats why i thought it´s a issue with the perl script or the
> trjconv / distance commands so that the wrong distances are extracted from the
> trajectories, but i couldn´t resolve it. I used the following trjconv command
> and the provided provided perl script:

Typo in the script.  In the gmx distance command, it should be -oall instead of 

> gmx trjconv -s pull.tpr -f traj_comp.xtc -o configs/conf.gro -sep // There was
> not traj.xtc file, only a traj_comp.xtc, any explanations?

New default naming.  I fixed the typo in the tutorial.  It should be traj_comp.xtc.



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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