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-us...@gromacs.org > > From: jalem...@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 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send > > a mail to gmx-users-requ...@gromacs.org. > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
