[gmx-users] Problems with pull simulation output - VMD shows broken up groups

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 3 11:50:20 CET 2011

Justin A. Lemkul wrote:
> Natalie Stephenson wrote:
>> Hi,
>> I've been having a problem with the pull simulation.  After the 
>> simulation is complete, I use trjconv to separate the pull file into 
>> seperate .gro's and load this into VMD.  When I view it in VMD as the 
>> 'video' continues parts of amino acids within the protein structure 
>> seem to jump a long way from the rest of that amino acid leaving a 
>> long bond between the two, which seems to remain there for the rest of 
>> the 'video'.  Can anyone tell me why this might be happening? And if 
>> there is a way of solving this problem?
>> I tried to have a look through the archive for this problem but I have 
>> no idea what to even search.
>> I would be immensely grateful for any light you could shed on this 
>> problem.

Sounds like FAQ #11.



>> Thanks in advance.
>> Natalie


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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