AMBER Archive (2009)

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

From: Marek Maly (marek.maly_at_ujep.cz)
Date: Wed Jun 10 2009 - 14:47:41 CDT

Dear prof. Case,
thank you very much for the valuable information !

   Best,

      Marek

Dne Wed, 10 Jun 2009 18:01:26 +0200 David A. Case
<case_at_biomaps.rutgers.edu> napsal/-a:

> 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_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> __________ Informace od NOD32 4051 (20090504) __________
>
> Tato zprava byla proverena antivirovym systemem NOD32.
> http://www.nod32.cz
>
> 

-- 
Tato zpráva byla vytvořena převratným poštovním klientem Opery:  
http://www.opera.com/mail/

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber