[gmx-users] umbrella sample Question

Justin Lemkul jalemkul at vt.edu
Fri Aug 18 19:04:49 CEST 2017

On 8/18/17 10:54 AM, yujie liu wrote:
> Hello,gromacs user
> I am a novice, I met some problems when I do this tutorial to learn umbrella sample, at http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html. I am using gromacs 5.1.4 and the summary_distances.dat file is not  complete while carrying out  ‘perl distances.pl’. Some values of distance between COM of Chain_A and Chain_B are empty and some distxxx.xvg files still existing. In fact, I checked out some distxxx.xvg and found which existed a value of distance but why these values can’t write into summary_distances.dat completely by commend ‘perl distances.pl’ ?  There is someone met with the situation??

People keep telling me that this happens and no one follows up with a 
solution.  I'd love to solve it once and for all, because I can never 
reproduce the problem.

Run gmx distance yourself, not from the script.  Something will fail and 
you'll get a clear error message that can be used to diagnose the 
issue.  Without that, it's impossible to help.




Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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