Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER in a rectangular box.
I did energy minimization successfully with following mdp file. -------------------------------------------------------------------------------------- ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions --------------------------------------------------------------------------------------- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. I did equilibration in NVT ensemble with following mdp file. -------------------------------------------------------------------------------------- title = NVT equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 7500000 ; 2 * 7500000 = 15 ns dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstxtcout = 1000 nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-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 cels nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; 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 = V-rescale ; modified Berendsen thermostat tc-grps = CHOL_DOPC SOL ; three coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 323 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 5 comm-mode = Linear comm-grps = CHOL_DOPC SOL --------------------------------------------------------------------------------------- After 15 ns NVT equilibration, I saw obtained file (nvt.gro) by VMD. Unfortunately, rectangular shape of box was converted to cylinder shape. DOPC and CHOL molecules moved from center of box to environs of box. What is reason of this issue? Should I use new parameters in mdp file? I am beginner in gromacs. Please help me to fix this issue. Any help will highly appreciated Best wishes -- 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