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