AMBER Archive (2005)

Subject: RE: AMBER: nmode

From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Thu Aug 04 2005 - 22:07:43 CDT


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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Wei Chen
> Sent: Thursday, August 04, 2005 11:04 AM
> To: amber_at_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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