AMBER Archive (2009)

Subject: Re: [AMBER] Thermodynamic parameters in mm_PBSA - NAB ?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jun 10 2009 - 11:01:26 CDT


On Wed, Jun 10, 2009, Marek Maly wrote:
>
> // get the normal modes:
> nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
>
> Temperature: 298.150
> Pressure: 1.000
>
> There is clearly written "Temperature", "Pressure" which can be set
> probably in function mm_options() - for example temperature using
> parameter TEMPI parameter.

This is not correct: TEMPI sets the initial velocity for a MD run; it has
nothing to do with with the thermochemistry set from normal modes.

Right now, the temperature for the normal modes thermodynamics is hard-wired:
look for the line "temperature = 298.15;" in nmode.c. You will have to change
this and recompile to get a different temperature. This should become an
input variable at some point.

>
> In mm_PBSA routine there is no chance (if I am not wrong) to set this
> thermodynamics parameters so
> there are probably used some defaults. But what if my simulations was
> done under slightly different
> conditions - for example T=310K instead defaul T=298K ?
>
> Just regarding TS calculation which is the output of NN mm_PBSA analysis.
> It is OK in this case just
> this transformation TS(310K)=310*TS(298K)/298 ...?

This assumes that S is itself temperature-independent, which is probably a
reasonable approximation over a small temperature range. But check this if
you can.

...dac

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