Hi again guys, Few more questions:
1. I would like to calculate compressibility of the protein+water system, but separating it into bulk water, hydration water and protein. So I need to pick these and compute volumes separately. When picking hydration water molecules, two tools are mentioned on the List: trjorder and g_hbond. Which one would you recommend for my task? 2. a)The program g_energy gives output for compressibility. What method was used for that calculation? b) When running g_energy I noticed a particularly crappy number for the specific heat of SPC water with ffgmx forcefield. It is about 17J/mol.K (should be about 75). I get similar number with my code using energy fluctuation method. Do you guys have any suggestions? I cut and paste my equilibration and production run mdp files. ---------------------------- Equilibration ---------------------------- Thanks, Frankie cpp = /lib/cpp define = -DPOSRES constraints = all-bonds integrator = md tinit = 0.0 dt = 0.001 ; ps ! nsteps = 10000 ; total 10 ps. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid comm-mode = Angular nstcomm = 1 comm-grps = System pbc = xyz coulombtype = PME rvdw = 0.9 rlist = 0.9 rcoulomb = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 275 ; Energy monitoring energygrps = System ; Pressure coupling is not on Pcoupl = no ; Random seed for Andersen thermostat andersen_seed = 815131 ; Generate velocites is on at 275 K. gen_vel = yes gen_temp = 275.0 gen_seed = 173529 ------------ NVT run ------------ cpp = /lib/cpp constraints = all-bonds integrator = md dt = 0.001 ; ps ! nsteps = 1100000 ; total 1.1ns. nstcomm = 1 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstlist = 10 ns_type = grid comm-mode = Angular nstcomm = 1 comm-grps = System pbc = xyz coulombtype = PME rvdw = 0.9 rlist = 0.9 rcoulomb = 0.9 fourierspacing = 0.12 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = System tau_t = 0.1 ref_t = 275 ; Energy monitoring energygrps = System ; Pressure coupling is not on Pcoupl = no ; Generate velocites is on at 275 K. gen_vel = yes gen_temp = 275.0 gen_seed = 173529 _______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php