On Thu, Dec 20, 2018 at 1:01 PM Gonzalez Fernandez, Cristina < cristina.gonzalezf...@unican.es> wrote:
> Hi Justin, > > > Do you think that the difference between a value of -280 ± 37 kj/mol > obtained by Gromacs and -367 kj/mol obtained by NAMD can be acceptable? > > As I said before, no, a massive difference like that, outside the error bars, is not acceptable. If you want more useful advice, you'll have to tell us exactly what you're doing and trying to compare. -Justin > > Thank you so much for all your help > > C. > > ________________________________ > De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> en nombre de Justin > Lemkul <jalem...@vt.edu> > Enviado: martes, 18 de diciembre de 2018 15:34:07 > Para: Discussion list for GROMACS users > Asunto: Re: [gmx-users] Running simulation differences > > On Tue, Dec 18, 2018 at 5:01 AM Gonzalez Fernandez, Cristina < > cristina.gonzalezf...@unican.es> wrote: > > > Hi again Justin, > > > > I've been thinking about the normal variability between MD simulations > you > > commented. I am simulating the interaction of a lipid with water, but the > > van der waals energy value that I obtain (-257.25 ± 35.86 kj/mol) for me > > is considerably different from the published value (-361 kj/mol). > However, > > according to your email maybe these values can be considered similar. Do > > you think my value and the published one are similar? How can I reduced > the > > error of the results because my value correspond to a long > > > I would not call those values similar at all. The two quantities you posted > before were within error of one another; those are similar. A difference of > over 100 kJ/mol, outside error, is enormous. You need to evaluate what > you're doing because in that case, I suspect something is inconsistent > between what is published and what you're doing. > > > > simulation (60 ns)? Could you recommend me a paper where is stated the > > common deviations/errors that are acceptable to a simulation result? > > > > There is none to my knowledge, and certainly can't be generalized. > Different quantities have different tolerances. Different software may > produce somewhat different results, as well. > > Also I wouldn't consider 60 ns long, by any means :) > > -Justin > > -- > > ========================================== > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > > ========================================== > -- > 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. > -- ========================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ========================================== -- 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.