[gmx-users] md step- structure fragmentation

[Mark Abraham]

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.

See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions 
for likely explanation and solution.

Mark
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