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

Natalie Stephenson Natalie.Stephenson at postgrad.manchester.ac.uk
Thu Mar 3 12:10:26 CET 2011

Thanks so much ... that's great!! :)  Hopefully problem solved!


From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: 03 March 2011 10:50
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Problems with pull simulation output - VMD shows broken up groups

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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