Hi
You can try 'autoimage' command in cpptraj.
Check the amber manual and search mail list for that. Let us know if you still can not solvr your issue.
Cheers
Hai
> On May 19, 2016, at 10:11 PM, Arati Paudyal <apsilwal123.gmail.com> wrote:
>
> Dear all,
>
> Just finished a long simulation of a protein-protein complex. But when I
> visualized the protein with VMD the entire protein changes the center and C
> terminal tail of one of the proteins slowly moved out of the water box,
> dangling out of the box. I researched and this looked like common problem
> when iwrap=1 is used. But my question is does it matter for all the
> analysis I just did i.e RMSD, energies,pressure .............? Do I need to
> run the entire simulation without iwrap?
>
> On one of the questions in amber list Jason had mentioned that it is just
> the visualization problem with vmd when iwrap is used. What do I do to
> recenter the protein? Does simply re-centering the protein solves the
> problem? or Do I need to rerun the simulation?
>
>
> &cntrl
> imin=0,
> irest=1,
> ntx=5,
> nstlim=40000000,
> dt=0.002,
> ntf=2,
> ntc=2,
> ntxo=2,
> ioutfm=1,
> temp0=300.0,
> tempi=300.0,
> ntpr=10000,
> ntwx=10000,
> ntwr=10000,
> cut=10.0,
> iwrap=1,
> ntb=2,
> pres0=1.0,
> ntp=1,
> taup=2.0,
> ntr=0,
> ntt=3,
> gamma_ln=1.0,
> ig=-1,
> /
>
> Thank you,
>
> RT
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Received on Thu May 19 2016 - 19:30:06 PDT
