Dear Justin, Thank you for your answer, I'm sorry for delay to reply. Actually I'm running a simulation of oil-water interface. I'm using Gromos 53a6 force field which is usually used for triglycerides. after semiisotropic and MD step I still have around 40 mN.m-1 interfacial tension which is pretty far from my experimental value. Following is my mdp file for NPT step. I would be very grateful if you can help me to solve this issue title = NPT equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 250000 ; 2 *250000 = 500 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; 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 = 2 ; accuracy of LINCS lincs_order = 2 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = SOL TRI ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of box vectors tau_p = 1.0 1.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, in bar compressibility = 0 4.5e-5 ; isothermal compressibility x,y axis/z axis 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 ; Velocity generation is off
On 19 April 2013 03:28, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/18/13 10:51 AM, Souilem Safa wrote: > >> Dear Gromacs users, >> I have runned a semiisotropic NPT simulation for a membrane, I have fixed >> the pressure in x and y axis and I varied it only in z axis to keep a >> stable interface. But after simulation the obtained interfacial tension is >> far bigger than the experimental value. Experimental is 27 mN.m-1 and the >> simulated one was around 38 mN.m-1. >> I will be very grateful if you can suggest me which parameters should I >> check in order to regulate the interfacial tension value. >> > > You haven't posted your .mdp file or even stated what force field you're > using. Is your force field designed to reproduce such surface tension > values? The results are only as good as the model itself, and your usage > of it. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
