Hi Justin,
Sorry for the misunderstanding. I am simulating the interaction of a lipid with water. I obtain practically the same value for the coulomb interaction energy, but I am not able to get a value for the van der waals energy close to the published one (although I have used the same settings than the ones used in the article). Therefore, I checked tha GMX manual and I tried to modified the settings that affect the van der waals energy in order to get a better value: vdwtype, vdw-modifier, rvdw and DispCorr (as I am using GROMOS96 FF I don't consider rvdw-switch). This is the .mdp file: title = Lipid A simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 5500000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 1.0 ps nstvout = 5000 ; save velocities every 1.0 ps nstenergy = 5000 ; save energies every 1.0 ps nstlog = 5000 ; update log file every 1.0 ps nstxtcout = 5000 xtc-grps = System ; Bond parameters continuation = yes ; restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 5 ; 20 fs, largely irrelevant with Verlet rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) rlist = 1.41 vdwtype = Cut-off vdw_modifier = None verlet-buffer-drift = -1 ; Electrostatics coulombtype = Reaction-Field ; Particle Mesh Ewald for long-range electrostatics epsilon_rf = 61 ; Temperature coupling is on tcoupl = nose-hoover ; modified Berendsen thermostat tc-grps = System ; two coupling groups - more accurate tau_t = 0.2 ; time constant, in ps ref_t = 298 ; reference temperature, one for each group, in K ; Pressure coupling is oN pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 0.5 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ;refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ;Dispersion correction ;DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 278 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed I would greatly appreciate if you could help me, because I don't know what else I can do, 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: jueves, 20 de diciembre de 2018 19:52:20 Para: Discussion list for GROMACS users Asunto: Re: [gmx-users] Running simulation differences 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. -- 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.