[gmx-users] Free solvation, problems with g_bar
samimishu at hotmail.com
Mon Nov 9 02:52:18 CET 2015
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
> 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 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
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