Hi Mikhail, I am using GMX4.5.5 to simulate SWM4-NDP polarizable water model, it is working fine. When i am running separately NA+ polarizable ion in SWM4-NDP water and Cl- polarizable ion in SWM4-NDP polarizable water model, it is working fine. But when I use the both NA+ and CL- (NaCl salt solution) polarizable model which is in conjuction with SWM4-NDP model, the RMS force is very large:
can anyone give some idea, what i am missing.. Thanking you Ananya here is my itp file [ defaults ] LJ Geometric [ atomtypes ] ;name mass charge ptype c6 c12 WO 15.99940 0.0 A 0.0 0.0 WH 1.00800 0.0 A 0.0 0.0 WS 0.0 0.0 S 0.0 0.0 WD 0.0 0.0 D 0.0 0.0 NAc 22.989769 0.0 A 0.0 0.0 NAs 0.0000000 0.0 S 0.0 0.0 CLc 35.45300 0.0 A 0.0 0.0 CLs 0.0000000 0.0 S 0.0 0.0 [ nonbond_params ] WO WO 1 3.67796770E-03 3.83182123E-06 WO NAc 1 7.84740725E-04 4.51332937E-07 WO CLc 1 6.24036649E-03 1.83075990E-05 NAc NAc 1 1.56840324E-04 4.66461074E-08 CLc CLc 1 9.08923242E-03 6.44595639E-05 NAc CLc 1 1.46880350E-03 2.62418143E-06 [ moleculetype ] ; molname nrexcl SM2 2 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 WO 1 SM2 OW1 1 1.71636 2 WH 1 SM2 HW2 1 0.55733 3 WH 1 SM2 HW3 1 0.55733 4 WD 1 SM2 DW 1 -1.11466 5 WS 1 SM2 SW 1 -1.71636 [ polarization ] 1 5 1 0.00097822 [ constraints ] ; i funct doh dhh 1 2 1 0.09572 1 3 1 0.09572 3 2 1 0.15139 [ virtual_sites3 ] 4 1 2 3 2 0.5 0.024034 [ exclusions ] ; iatom excluded from interaction with i 1 2 3 4 5 2 1 3 4 5 3 1 2 4 5 4 1 2 3 5 5 1 2 3 4 [ moleculetype ] ; molname nrexcl NA+ 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 NAc 1 NA NAc 1 1.687597 2 NAs 1 NA NAs 1 -0.687597 [ polarization ] ; See notes above. alpha (nm^3) 1 2 1 0.000157 [ exclusions ] ; iatom excluded from interaction with i 1 2 2 1 [ moleculetype ] ; molname nrexcl Cl- 1 [ atoms ] ; id at type res nr residu name at name cg nr charge 1 CLc 1 ion CLc 1 2.457187 2 CLs 1 ion CLs 1 -3.457187 [ polarization ] ; See notes above. alpha (nm^3) 1 2 1 0.003969 [ exclusions ] ; iatom excluded from interaction with i 1 2 2 1 here is my g.mdb file include = define = integrator = md tinit = 0 dt = 0.0005 nsteps = 1000000 init_step = 0 simulation_part = 1 comm-mode = Linear nstcomm = 10 comm-grps = system bd-fric = 0 ld-seed = 1993 emtol = 0.1 emstep = 0.01 niter = 30 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 10 nstvout = 00 nstfout = 0 nstlog = 50 nstcalcenergy = -1 nstenergy = 10 nstxtcout = 250 xtc-precision = 1000 xtc-grps = energygrps = System nstlist = 5 ns-type = grid pbc = xyz rlist = 0.75 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 0.75 epsilon_r = 1 epsilon_rf = 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 0.75 DispCorr = EnerPres table-extension = 1 energygrp_table = fourierspacing = 0.12 fourier_nx = 32 fourier_ny = 32 fourier_nz = 32 pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no gb_algorithm = Still nstgbradii = 0 rgbradii = 0 gb_saltconc = 0 implicit_solvent = No tcoupl = nose-hoover nsttcouple = -1 nh-chain-length = 10 tc-grps = system tau-t = 0.05 ref-t = 300 gen-vel = yes gen-temp = 300 gen-seed = 173529 constraints = all-bonds constraint-algorithm = shake continuation = no Shake-SOR = no shake-tol = 0.0001 lincs-order = 4 lincs-iter = 2 lincs-warnangle = 30 morse = no energygrp_excl = nwall = 0 wall_type = 9-3 wall_r_linpot = -1 wall_atomtype = wall_density = wall_ewald_zfac = 3 pull = no disre = No disre-weighting = Conservative disre-mixed = no disre-fc = 1000 disre-tau = 0 nstdisreout = 100 orire = no orire-fc = 0 orire-tau = 0 orire-fitgrp = nstorireout = 100 dihre = no dihre-fc = 1000 free-energy = no init-lambda = 0 delta-lambda = 0 foreign_lambda = sc-alpha = 0 sc-power = 0 sc-sigma = 0.3 nstdhdl = 10 separate-dhdl-file = yes dhdl-derivatives = yes dh_hist_size = 0 dh_hist_spacing = 0.1 couple-moltype = couple-lambda0 = vdw-q couple-lambda1 = vdw-q couple-intramol = no userreal4 = 0 -- 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
