From: David A Case <>
Date: Sat, 23 Jul 2016 08:11:01 -0600

On Sat, Jul 23, 2016, nida baig wrote:
> In the context of your reply, attach is the image of the protein in
> water box. After visualization what would you suggest should I repeat
> the simulation with large solvent box or if I ignore it , will the
> results and analysis be affect Dr Nida Baig

Something looks wrong here: have you imaged the simulation using the
"autoimage" command in cpptraj? Have you done a constant pressure
equilibration? The density of solvent at the right side of the image looks
very low --people on the mailing list are probably not going to help very much
here: you will have to carefully explore the behavior of your simulation.


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Received on Sat Jul 23 2016 - 07:30:02 PDT
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