Dear Justin, Even with the new force field I am getting the same result. The methanol. gro file , em.mdp, pr,mdp and md.mdp files looks like these Methanol, 1 bar, 300K, equilibrated using PME, BdG 21-09-2001 648 1MeOH Me1 1 1.970 1.460 1.209 -0.8587 -0.1344 -0.0643 1MeOH O2 2 1.978 1.415 1.082 0.0623 -0.1787 0.0036 1MeOH H3 3 1.905 1.460 1.030 -0.5020 -0.9564 0.0997 2MeOH Me1 4 2.013 0.181 0.123 0.0317 0.4268 -0.0034 2MeOH O2 5 1.980 0.097 0.224 -0.8424 -0.0021 -0.6308 2MeOH H3 6 2.060 0.100 0.284 -0.7967 -0.7548 -0.6455 3MeOH Me1 7 2.008 0.409 0.498 -0.6920 0.4374 0.2455 3MeOH O2 8 2.109 0.460 0.422 -0.6105 0.1049 0.1322 3MeOH H3 9 2.170 0.506 0.486 -0.6959 -1.9809 1.8452 4MeOH Me1 10 1.856 1.779 1.151 -0.2574 0.2271 -0.0352 4MeOH O2 11 1.951 1.877 1.153 0.0214 -0.0482 0.2841 EM.mdp.... ; VARIOUS PREPROCESSING OPTIONS = title = mellitin cpp = /lib/cpp define = -DFLEXIBLE ; RUN CONTROL PARAMETERS = integrator = steep ; start time and timestep in ps = tinit = 0 dt = 0.001 nsteps = 4000 nstlist =10 ns_type =grid rlist =0.5 rcoulomb =1.4 vdwtype =cutoff rvdw =0.8 ; ENERGY MINIMIZATION OPTIONS = emtol = 0.00001 emstep = 0.1 nstcgsteep = 1000 PR.mdp..... warnings = 10 cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1000 ; total 1.0 ps. nstcomm = 1 nstxout = 10 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.5 rcoulomb = 1.4 rvdw = 0.8 epsilon_r = 66 ; Berendsen temperature coupling is on in two groups Tcoupl = nose-hoover tau_t = 0.1 0.1 tc-grps = Protein other ref_t = 300 300 ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 MD.mdp... cpp = /lib/cpp constraints = all-bonds integrator = md tinit = 100 dt = 0.002 ; ps !leapfrog algorithm 2fs timestep nsteps = 1000000 ; total 2 ns. nstcomm = 1 nstxout = 10000 nstvout = 5000 nstfout = 0 nstlist = 10 ns_type = grid rlist = 0.5 rcoulomb = 1.4 rvdw = 0.8 epsilon_r = 66.0 ; Berendsen temperature coupling is on in two groups Tcoupl = Berendsen tau_t = 0.1 0.02 tc-grps = protein other ref_t = 300 300 solvent_optimization = sol ; Energy monitoring energygrps = Protein other ; Pressure coupling is not on Pcoupl = Berendsen tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 ------------------------------------------------------------------------------------ I have mailed the itp for methanol that I am using in my previous mail. Kindly give me advice as to why I am getting similar results for water and methanol. Thanks.. sharada
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
