AMBER Archive (2004)

Subject: Re: AMBER: temperature in DelPhi for MM-PBSA calculation

From: rluo_at_uci.edu
Date: Mon Feb 02 2004 - 20:45:52 CST

If the ionic strength is nonzero, you have to redo it with the
correction temperature, though I don't think the energy difference would
be very large for a temperature difference of 25K.

If not, the PB energy is independent of the temperature if you assume
that dielectric constants and atomic radii do not depend on temperature.

Best,

Qing Zhang wrote:
> Dear Amber users:
>
> I used DelPhi for computing polar solvation free
> energy in MM-PBSA module, and just find out that
> DelPhi results are based on 25 Celsius temperature
> (298 K, set in DelPhi's source code). My systems were
> simulated at 0 Celsius in Amber and I have already
> computed the solvation free energies. Is there any
> easy way to adjust the values of these energies
> correctly due to the temperature difference? I don't
> wanna go though the time-consuming energy computations
> again.
>
> Thanks,
>
> Qing Zhang
>
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-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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