[gmx-users] Free solvation, problems with g_bar

[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
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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> Department of Pharmaceutical Sciences
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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