[gmx-users] md step- structure fragmentation

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 29 05:22:01 CET 2012

On 29/02/2012 3:10 PM, priya thiyagarajan wrote:
> hello sir,
> I performed simulation for 30ns, because of queue time limit my run terminated at 11.6ns..
> i thought of analysing my trajectory file.. so generated pdb file from trr using dump option..
> when i visualize the pdb,i noted that my protein structure got fragmented..
> when i visualize my npt and nvt structure ,its looking good.. but my md structure getting framented..
> what is the possible reason for this fragmentation.

for likely explanation and solution.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120229/33698c5f/attachment.html>

More information about the gromacs.org_gmx-users mailing list