Lara,
I'm willing to bet that it's a visualization issue. Your protein is
drifting out of your box, but since you have PME enabled, another version
of it will drift back into your box- someone might be able to give a better
explaination.
Try loading it VMD with a PME box, or centering it first with cpptraj with
the autoimage command.
Best,
Kenneth
On Friday, July 10, 2015, Lara rajam <lara.4884.gmail.com> wrote:
> Dear Amber !
>
> I am doing a simulation of a protein complex.
> the protein is having two chains A and B and a ligand.
>
> I did md for 20 ns in NPT ., when I converted the final md.rst file to pdb
> and viewed it
> the protein chains split apart . what is the mistake I am doing
>
> i used the following input file !
>
> Molecular_dynamics for 5 ns
>
> &cntrl
>
> imin = 0, irest = 1, ntx = 7,
>
> ntb = 2, pres0 = 1.0, ntp = 1,
>
> taup = 2.0,
>
> cut = 10, ntr = 0,
>
> ntc = 2, ntf = 2,
>
> tempi = 300.0, temp0 = 300.0,
>
> ntt = 3, gamma_ln = 1.0,
>
> nstlim = 5000000, dt = 0.001,
>
> ntpr = 1000, ntwx = 1000, ntwe = 1000,
>
> iwrap=1
>
> /
>
>
> attached the image
>
>
>
> comments will improve my understanding !
>
>
> thank you !
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Jul 10 2015 - 08:00:03 PDT
