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

[Natalie Stephenson]

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

Natalie


________________________________________
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.

http://www.gromacs.org/Documentation/FAQs

-Justin

>> Thanks in advance.
>> Natalie
>>
>>
>

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110303/6225a2d3/attachment.html>