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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 06 2009 - 08:35:15 PDT
