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Thanks so much ... that's great!! :) Hopefully problem solved!<br>
<br>
Natalie<br>
<br>
<br>
________________________________________<br>
From: gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Justin A. Lemkul [jalemkul@vt.edu]<br>
Sent: 03 March 2011 10:50<br>
To: Discussion list for GROMACS users<br>
Subject: Re: [gmx-users] Problems with pull simulation output - VMD shows broken up groups<br>
<br>
Justin A. Lemkul wrote:<br>
><br>
><br>
> Natalie Stephenson wrote:<br>
>><br>
>> Hi,<br>
>><br>
>> I've been having a problem with the pull simulation. After the<br>
>> simulation is complete, I use trjconv to separate the pull file into<br>
>> seperate .gro's and load this into VMD. When I view it in VMD as the<br>
>> 'video' continues parts of amino acids within the protein structure<br>
>> seem to jump a long way from the rest of that amino acid leaving a<br>
>> long bond between the two, which seems to remain there for the rest of<br>
>> the 'video'. Can anyone tell me why this might be happening? And if<br>
>> there is a way of solving this problem?<br>
>><br>
>> I tried to have a look through the archive for this problem but I have<br>
>> no idea what to even search.<br>
>><br>
>> I would be immensely grateful for any light you could shed on this<br>
>> problem.<br>
>><br>
><br>
<br>
Sounds like FAQ #11.<br>
<br>
http://www.gromacs.org/Documentation/FAQs<br>
<br>
-Justin<br>
<br>
>> Thanks in advance.<br>
>> Natalie<br>
>><br>
>><br>
><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>
<br>
========================================<br>
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