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

Justin A. Lemkul jalemkul at vt.edu
Thu Mar 3 11:49:38 CET 2011

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


More information about the gromacs.org_gmx-users mailing list