[gmx-users] Umbrella sampling

[Justin Lemkul]

On 6/14/17 10:52 PM, Kingsley Theras Primus Dass . wrote:
> Hii
>   I am trying out the umbrella sampling tutorial. I finished generating a
> series of coordinate file , but when i run the perl script the
> summary_distance.dat doesnt generate the COM distance value ....
> What would be the possible reason for this ?
> 

People keep reporting this and I never find out why, but the advice is the same 
- abandon the script and try one of the calls to gmx distance yourself.  It will 
print an error that you can diagnose.  Probably your index file isn't set up 
correctly.  If you do work it out, please report back so I know if there's 
actually something wrong (the script itself is quite trivial so I know that's 
not the problem, but maybe something about the call to gmx distance is).

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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