- you didn't do an energy minimization - you used hz1 0 and I used hz1 1.0 - you didn't include make hole options hr,hx,hy
*** Somebody already suggested nstlog = 1 and nstenergy = 1, please try that!!! In fact make everything 1 (nstxout,nstxtcout,...) Here is what worked for me with the same POPE file: 1. Do an energy minimization 2. run the make_hole mdrun: grompp -maxwarn 10000 -f grompp_md.mdp -c a.gro -p a.top -o a.tpr mdrun -nice 4 -hole -holep hole.mdp -s a.tpr -o a.trr -c b.gro -g output.mdrun -v -x a.xtc ############################# em.mdp ############################ title = energyMinimization cpp = /usr/bin/cpp integrator = steep nsteps = 500 emtol = 200 emstep = 0.000005 comm_mode = linear nstcomm = 1 comm_grps = System ns_type = grid pbc = xyz coulombtype = PME fourierspacing = 0.15 pme_order = 4 vdwtype = switch rvdw_switch = 0.9 rvdw = 1.0 rlist = 1.1 DispCorr = no Pcoupl = no tcoupl = no annealing = no gen_seed = 9896 constraints = hbonds constraint_algorithm= shake shake_tol = 0.0001 ############################# hole.mdp ############################ holetype = Grasp_ascii hfm = 10 supf = 10 molsurf_log = make_hole.log hr = 0 hx = 0 hy = 0 hz = 3.5 hp1 = 1 hp2 = 17680 s1 = 17681 s2 = 43934 hz1 = 1.0 hz2 = 6.0 sfm = 10.0 sofs = 0 molsurf_file = pagpsys_tot_e.surf debugsurf = no resforces = yes ############################ run.mdp ################################# title = seriousMD cpp = /usr/bin/cpp define = -DPOSRES integrator = md nsteps = 10000 tinit = 0 dt = 0.002 comm_mode = None nstcomm = 1 comm_grps = System nstxout = 10000 nstvout = 10000 nstfout = 10000 nstlog = 100 nstlist = 10 nstenergy = 10000 nstxtcout = 250 ns_type = grid pbc = xyz coulombtype = Cut-off ;fourierspacing = 0.15 ;pme_order = 4 vdwtype = switch rvdw_switch = 0.9 rvdw = 1.1 rlist = 1.1 rcoulomb = 1.1 DispCorr = no Pcoupl = Berendsen tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1. tcoupl = nose-hoover tc_grps = POPE SOL tau_t = 0.05 0.05 ref_t = 300. 300. annealing = no gen_vel = yes gen_temp = 300. gen_seed = 9896 constraints = hbonds constraint_algorithm= shake shake_tol = 0.0001 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
