[gmx-users] umbrella sample Question

[Justin Lemkul]

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

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

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