[gmx-users] md step- structure fragmentation

priya thiyagarajan priya.thiyagarajan09 at gmail.com
Wed Feb 29 05:10:31 CET 2012

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.

can anyone please help me with your answer..

also please give an idea how to eliminate this error..

Thanking you,
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