Hello everybody, I have many difficulties to reproduce TIP3P simulation results with CHARMM TIP3P. Regular TIP3P gives systematically a lower density than its CHARMM counterpart, independantly from the cutoff for non-bonded interactions, the version of GROMACS (4.5.1 or 4.0.7) or the double precision. Regular 961,067 +/-0,756 g/L CHARMM 980,860 +/-0,492 g/L
The Enthalpy of vaporization follows a similar scheme: regular -39,992 +/-0,021 kJ/mol CHARMM -40,665 +/-0,009 kJ/mol In fact, CHARMM gives results closer to what I should obtain at 300K and 1 bar for TIP3P. I suspect an issue with the bond constraints, but I can't locate precisely where it is. Settle parameters are exactly the same (as well as constraints for flexible water). Did someone ever face a similar problem? Rgards, Nicolas P.S. I My system is just a box of 1728 water molecules pre-equilibrated for 500 ps at 300 K and 1 bar. P.S. II I'm using the following simulation parameters: constraints = hbonds constraint_algorithm = LINCS continuation = no lincs-order = 4 lincs-iter = 1 lincs-warnangle = 30 morse = no (LINCS or SHAKE should not make any difference since TIP3P is normally treated by SETTLE). Other parameters are: ; COUPLING ; Temperature coupling tcoupl = Berendsen nsttcouple = -1 nh-chain-length = 10 tc_grps = System tau_t = 0.1 ref_t = 300 ; Pressure coupling pcoupl = Berendsen pcoupltype = isotropic nstpcouple = -1 tau_p = 1 compressibility = 4.5e-5 ref_p = 1 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ns_type = grid pbc = xyz rlist = 1.15 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.15 vdwtype = Cutoff rvdw = 1.0 fourierspacing = 0.10 pme_order = 6 ewald_rtol = 1.0e-6 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = yes ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 200000 comm_mode = Linear nstcomm = 1 comm_grps = System -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44/53 -- 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
