Hi, Yong,
Thank you for your reply. Did you mean the entropy is not significant for free
energy? Does quasiharmonic method take less memory?
Thank you!
Wei
ÒýÓÃ Yong Duan <duan.ucdavis.edu>:
>
> Nmode on 10,000-atom probably takes long time, even if you do have plenty of
> memory.
> Option 1) Don't calculate it (I am not kidding).
> Option 2) Quasi-harmonic (principle component) method from MD trajectory.
>
>
> Yong
>
> -----Original Message-----
> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
> Wei Chen
> Sent: Thursday, August 04, 2005 11:04 AM
> To: amber.scripps.edu
> Subject: AMBER: nmode
>
>
> Hi, Guys,
>
> I have a big system about 10,000 atoms. I want to use mm_pbsa to calculate
> free energy. But I have no enough memory for entropy calculation by nmode.
>
> Does anybody have ideas to calculate entropy in different ways?
>
> Thanks!
>
> Wei Chen
>
>
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Received on Fri Aug 05 2005 - 04:53:01 PDT
