Dear Carlos,
Thanks for your reply. However, I don't quite understand how should I do
that. I looked into the manual about ptraj however can't find any
explanation. Can you explain a bit more please? Thanks very much.
Best regards,
Kailee
On 3/21/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> if you are calcualting diffusion behavior you imght not want to image.
>
> ptraj might work- it may be that all of the copies are in the same
> residue,
> Tom Cheatham would know if ptraj can image by atom or only by residue.
>
> On 3/21/07, Kailee <kaileeamber.googlemail.com> wrote:
> > Dear all,
> >
> > I have done a 1ns md simulation (seperated into 10 calculations) of
> hydrogen
> > molecule diffusion into a big protein using LES method. And I have made
> 1000
> > LES copies of the hydrogen molecule. Now I want to analyse the
> trajectory
> > files. When I load the trajectories into VMD, I found that there are
> many
> > hydrogen molecules flied out of the primary box, can I ask how can I
> reimage
> > them back to the central box? what is the difference in doing so between
> the
> > simulations with and without LES method?
> >
> > Thanks very much for any suggestions.
> >
> > Best regards,
> > Kailee
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling.gmail.com
> Stony Brook, NY 11794-5115
> ===================================================================
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Received on Sun Mar 25 2007 - 06:07:14 PDT
