Hello, I'd like to run a position restrained MD of a protein in water with 3000 (protein) + 40000 (SOL) atoms.
I preprocess the input with the command line: $grxdir/grompp -f 4AKEprePRMD.mdp -po 4AKE_PRMD.mdp -c 4AKE_EMcg.gro -p 4AKEallHion.top -pp 4AKEprePRMD.top -o 4AKE_PRMD.tpr 4AKEprePRMD.mdp is: title = 4AKE_PRMD cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 5000 ; total 10.0 ps. nstcomm = 1 ; [steps] frequency for center of mass motion removal nstxout = 100 ; [steps] frequency to write coordinates to output trajectory file nstvout = 100 ; [steps] frequency to write velocities to output trajectory nstfout = 0 ; [steps] frequency to write forces to output trajectory nstlog = 10 ; [steps] frequency to write energies to log file nstenergy = 10 ; [steps] frequency to write energies to energy file nstlist = 5 ; neighbour searching ns_type = grid rlist = 1.0 coulombtype = EWALD rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tau_t = 0.1 0.1 tc-grps = Protein Non-Protein ref_t = 300 300 ; Energy monitoring energygrps = Protein SOL ; Pressure coupling is on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ; [1/bar] compressibility of water ref_p = 1.0 ; [bar] reference pressure for coupling ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 Then I run the PR MD: $grxdir/mdrun -s 4AKE_PRMD.tpr -o 4AKE_PRMD.trr -c 4AKE_PRMD.gro -e 4AKE_PRMD.edr -g 4AKE_PRMD.log -v These lines appear on the terminal: starting mdrun 'Protein in water' 5000 steps, 10.0 ps. ...but from this point on nothing more is displayed. I see neither steps nor time left. Are the parameter in the mdp file defining a too expensive simulation? I've tryied removing pressure and temperature coupling but the problem remains. How can I solve this issue? -DPOSRES refers to posre.itp, I guess. posre.itp was created from the original pdb before the energy minimization. Should I run pdb2gmx once again after the EM to create a new posre.itp? Thanks, Stefano _______________________________________________ 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
