AMBER Archive (2006)

Subject: RE: AMBER: question on protein folding simulation

From: Yong Duan (
Date: Tue Dec 05 2006 - 13:57:45 CST

Dear Noriaki,

This suggestion is quite useful, at least at the beginning.

But if you insist on folding simulation using explicit water from the
extended conformation or if you need to consider the expansion, you need to
reduce/increase the box size at some point. For velocities, as Carlos
suggested, there are velocities in the restart file. When you remove the
"excessive" water, you can keep both coordinates and the velocities. If you
use tleap to re-generate topology file, you can append the velocities to the
end of the coordinates along with the box information.

The system is actually a bit discontinuous after removal/addition of water
because the water molecules at the surface of the box need to adjust to
their "new" interactions. But the water around the protein retains the
interactions and velocities reasonably well. If you do not want the
discontinuity, you then have to run the simulations without changing the


> -----Original Message-----
> From:
> [] On Behalf Of Noriaki Okimoto
> Sent: Sunday, December 03, 2006 6:51 PM
> To:
> Subject: Re: AMBER: question on protein folding simulation
> Hi.
> Thanks for your reply.
> Now I would like to try folding simulation with using explicit water
> molecules.
> Anyway, thanks.
> Regards,
> Noriaki Okimoto
> >I donot know whether I am right. Can you di the
> >simulation without water box, and after it is
> >partially folded, you add a water box? Maybe this
> >method will be much better.
> >
> >Best regards.
> >

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