Dear Gromacs users, I am trying to perform a MD simulation in gromacs 4.5.4 using a protein and ligand in gas phase. I have previously run the simulation in water without any problem. Now, I want to compare the result to see the effect of solvent.
But for running the same simulation after stripping the waters from the simulation box I am looking for some advise. I am having following issues: a) If I use 'md' i.e usual leap frog integrator with nstcomm=10 and comm-mode=Linear( this was the setup I had when I ran the simulation in water), I find after running the system of protein and ligand in gas phase for some time ( about 1 ns ), the protein starts rotating i.e it generates a very high angular momentum. b) So, I thought of using comm-mode=angular,,, But then grompp gives me a warning that removing rotation is not a problem only if I have only 1 molecule in the system ...which is not the case here as I have ligand and some ions . Any suggestion is highly appreciated. I can change nstcomm=1 using comm-mode=Linear but I am not sure it will stop the rotation of the protein about its own axis. I am running the system using periodic boundary condition and using PME for electrostatics. c) another option I thought of was using 'sd' integrator but considering my simulation in water having been performed using md integrator, I was looking to keep my .mdp file option as similar as possible in both cases. Any help on how to perform the simulations in gas-phase will be highly appreciated. Here is my current .mdp options: title = Umbrella pulling simulation ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 1500000 ; 800 ps nstcomm = 10 ; Output parameters nstxout = 0000 ; every 10 ps nstvout = 0000 nstfout = 0000 nstxtcout = 250 nstenergy = 250 ; Bond parameters constraint_algorithm = lincs constraints = hbonds continuation = yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = System tau_t = 0.5 ref_t = 300 ; Pressure coupling is on Pcoupl = no pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on gen_vel = yes ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres Thanks Sanku -- 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
