[gmx-users] Tools for energy of solvation in polimers

[Mishelle Oña]

 OK I understand, so you think I couldn´t use Gromacs to calculate the Energy of Solvation? If that is the case could you help me with a tutorial or other tipe of information that could help me with this staff. Please I have been struggling with this for weeks. I need to solve it 
 Mishelle

> > To: gmx-users at gromacs.org
> > From: jalemkul at vt.edu
> > Date: Sun, 8 Nov 2015 20:38:18 -0500
> > Subject: Re: [gmx-users] Free solvation, problems with g_bar
> > 
> > 
> > 
> > On 11/8/15 8:35 PM, Mishelle Oña wrote:
> > >   Hi everybody!I am calculating the energy of solvation of a polimer (polilactic acid.) I have a simulation of 40 000 frames and I am taking random frames of the simulation to aply the free energy tutorial of gromacs. When I perform the g_bar tool this message:WARNING: Some of these results violate the Second Law of Thermodynamics appears at the end. Do you have any idea of what is wrong? or any advice about this problem?
> > 
> > As I already told you several days ago, an alchemical transformation on a 
> > polymer is unlikely to converge or give sensible results.  You shouldn't 
> > approach your problem in this way.
> > 
> > -Justin
> > 
> > -- 
> > ==================================================
> > 
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > 
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> > 
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> > 
> > ==================================================
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