Hi Berk,
Maybe try to run with both and see what happens ;-) ... As the manual
says, when yo set the parameter to 1, calculation of the entropy using
the quasi-harmonic approximation is performed. Needless to say, you
should sit down with literature (and also other threads about this topic
on this list) before seriously attempting this type of calculation.
Best wishes
Vlad
On 06/01/2015 08:25 AM, Ramin Ekhteiari wrote:
> Hi Dears,
> I try to calculate the binding free energy of a complex.If I am wrong, please correct me, as I know in this estimation, entropy component is neglected, but I have come across to following option in amber manual:
> """entropy : Specifies whether or not a quasi-harmonic entropy approximation is made with ptraj.
> Allowed values are 0: Don’t. 1: Do (Default = 0)"""
> What does this mean?? If I assign 0/1 what does it happen?
> Would be grateful for any advice.
> Berk.
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 01 2015 - 00:30:02 PDT
