[gmx-users] g_energy -fee

[David van der Spoel]

On Wed, 2003-09-17 at 09:30, Ilya Chorny wrote:
> I guess I need to  be more specific. How does it calculate the free energy?
> 

g_energy -h :

With -fee an estimate is calculated for the free-energy difference with
an
ideal gas state:
  Delta A = A(N,V,T) - A_idgas(N,V,T) = kT ln < e^(Upot/kT) >
  Delta G = G(N,p,T) - G_idgas(N,p,T) = kT ln < e^(Upot/kT) >
where k is Boltzmann's constant, T is set by -fetemp andthe average is
over the
ensemble (or time in a trajectory). Note that this is in principle only
correct
when averaging over the whole (Boltzmann) ensemble and using the
potential
energy. This also allows for an entropy estimate using:
  Delta S(N,V,T) = S(N,V,T) - S_idgas(N,V,T) = (<Upot> - Delta A)/T
  Delta S(N,p,T) = S(N,p,T) - S_idgas(N,p,T) = (<Upot> + pV - Delta G)/T
 
When a second energy file is specified (-f2), a free energy difference
is
calculated dF = -kT ln < e ^ -(EB-EA)/kT >A , where EA and EB are the
energies
from the first and second energy files, and the average is over the
ensemble A.
NOTE that the energies must both be calculated from the same trajectory.
 
O


> Thanks
> 
> Ilya
> 
> 
> 
> -----Original Message-----
> From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
> Behalf Of David van der Spoel
> Sent: Wednesday, September 17, 2003 12:45 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_energy -fee
> 
> 
> On Wed, 2003-09-17 at 01:17, Ilya Chorny wrote:
> > Could someone explain to what the -fee does in g_energy.
> > 
> Have you run 
> g_energy -h ?
> > 
> > Thanks
> > 
> > Ilya
> > 
> > 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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