Hi Iman, What version of Gromacs are you using? What is the error message?
Dan On Tue, Aug 29, 2017 at 1:27 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com > wrote: > Dear Dan, > > I have attached the NPT.mdp file in the following: > > title = NPT equilibration > ; Run parameters > integrator = md > nsteps = 20000000 > dt = 0.001 > > ; Output control > nstxout = 500 > nstvout = 500 > nstenergy = 500 > nstlog = 500 > > ; Bond parameters > continuation = no > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 1 > lincs_order = 4 > > ; Neighborsearching > cutoff-scheme = Verlet > ns_type = grid > nstlist = 20 > rlist = 2.0 > rcoulomb = 2.0 > rvdw = 2.0 > > ; Electrostatics > coulombtype = PME > pme_order = 4 > fourierspacing = 0.12 > > ; Temperature coupling is on > tcoupl = V-rescale > tc-grps = system > tau_t = 0.1 > ref_t = 298.15 > > ; Pressure coupling is on > pcoupl = berendsen > pcoupltype = surface-tension > tau_p = 2.0 2.0 > ref_p = 1440 1.0 > compressibility = 4.46e-5 0 > refcoord_scaling = com > > ; Periodic boundary conditions > pbc = xyz > > ; Dispersion correction > DispCorr = EnerPres > > ; Velocity generation > gen_vel = yes > lincs_warnangle = 90 > > > Now I'm gonna using semiisotropic instead of surface tension like in the > following: > pcoupltyp = semiisotropic > tau_p = 0.5 > ref_p = 1.0 1.0 > compressibility = 4.46e-5 0 > > Thank you for your help. > Sincerely, > Iman > > On Tue, Aug 29, 2017 at 6:04 PM, Iman Ahmadabadi < > imanahmadabad...@gmail.com > > wrote: > > > Dear All Users, > > > > I'm calculating the surface tension of the water, my box contains almost > > 5000 water molecule in the middle of that. Through NVT equilibration, I > got > > reasonable results for surface tension but when I use NPT for my system, > > the system crashes every time. The pressure coupling options are in the > > following: > > > > pcoupltyp = surface-tension > > tau_p = 0.5 0.5 & 1.0 1.0 & 2.0 2.0 (Crashing with all > > three values) > > ref_p = 1440 1.0 > > compressibility = 4.46e-5 0 > > > > first ref-p value is 720*2 = 1440. 720 is the surface tension of water in > > 298.15. > > > > Now, I'm going to use semiisotropic for P-coupling: > > > > pcoupltyp = semiisotropic > > tau_p = 0.5 > > ref_p = 1.0 1.0 > > compressibility = 4.46e-5 0 > > > > Could I have any recommendation about my problem with surface-tension > > pcoupltyp? Am I right with semiisotropic options? > > > > > > Respectfully, > > Iman Ahmadabadi > > > > > > -- > Iman Ahmadabadi > > Sharif University of Technology, Tehran, Iran > > Department of Physics and Chemistry > > Phone: (+98) 9156125273 > > Email: imanahmadabad...@gmail.com , ahmadabad...@ch.sharif.edu > -- > 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.
