[gmx-users] tutorial umbrella sampling

Matthias Kiesel matze.kiesel at gmail.com
Mon Nov 30 20:17:39 CET 2015

Thanks,  that did the trick! Now everything works fine.

Am 29.11.2015 um 12:00 schrieb 
gromacs.org_gmx-users-request at maillist.sys.kth.se:

> 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
> -oxyz.
>> 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

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