AMBER Archive (2006)

Subject: Re: AMBER: question on protein folding simulation

From: Noriaki Okimoto (okimoto_at_gsc.riken.jp)
Date: Thu Dec 07 2006 - 06:25:51 CST

Hi,
Thank your for many suggestions.
I fully consent your suggestions, and I will try!

Thanks.

Noriaki

>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
>box.
>
>
>yong
>
>
>
>>-----Original Message-----
>>From: owner-amber_at_scripps.edu
>>[mailto:owner-amber_at_scripps.edu] On Behalf Of Noriaki Okimoto
>>Sent: Sunday, December 03, 2006 6:51 PM
>>To: amber_at_scripps.edu
>>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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