Dear gmx users, I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system. I'd prefer to run the equilibrium steps with position restraints on water oxygen atoms, because the water molecules penetrate the lipid bilayer when running the equilibrium and I don't want it to happen. I tried the NVT with position restraints on water by adding -DPOSRES_WATER to nvt.mdp file and editing the top file by changing the fc to 100000.
#ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 100000 100000 100000 #endif This edition turned into a better result. Now I tried to put such a restraint on npt but the gromacs does not allow it by turning a fatal error: A charge group moved too far between two domain decomposition steps. npt.mdp file: ;NPT equlibration Dimer-POPC-Water - CHARMM36 define = -DPOSRES_LIPID -DPOSRES -DPOSRES_WATER ; P headgroups of POPC and Protein is position restrained (uses the posres.itp file information) integrator = md ; leap-frog integrator nsteps =1000000 ; 1 * 1000000 = 1000 ps dt = 0.001 ; 1 fs ; Output control nstxout = 2000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) vdwtype = switch rvdw_switch = 1.0 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein_POPC Water_Ces_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 ; time constant, in ps ref_t = 310 310 ; reference temperature, one for each group, in K pcoupl = Berendsen ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 310 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = Protein_POPC Water_Ces_CL refcoord_scaling = com I am wondering how it is possible to prevent penetrating the water molecules through equilibrium? And how I can put the restraint in npt as well as nvt? Would you please help me in this issue please? Sincerely, Shima -- 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
