AMBER Archive (2004)

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

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Mon Feb 02 2004 - 18:58:54 CST

I already made the change in the script
mm_pbsa_statistics.pm during my previous calculation.

But I don't know if kT is just for unit conversion or
used in solving PB equation in DelPhi, because I see
the conversion is used in many places of DelPhi source
code besides the output part.

Thanks,

Qing

--- "S. Frank Yan" <SYan_at_gnf.org> wrote:
> The unit of electrostatic energy in DelPhi is kT, so
> it will be easy for
> you to convert to whatever temperature you want. In
> fact, the mm_pbsa
> script has a default temperature of 300 K, which can
> be specified,
> though not recommended, by the user. The file is:
>
> $AMBERHOME/src/mm_pbsa/mm_pbsa_statistics.pm
>
> at around line 50. Good luck, Frank
>
>
>
> -----Original Message-----
> From: Qing Zhang [mailto:qingzhang_nyu_at_yahoo.com]
> Sent: Monday, February 02, 2004 2:54 PM
> To: amber_at_scripps.edu
> Subject: AMBER: temperature in DelPhi for MM-PBSA
> calculation
>
> 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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