Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box.
I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, 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. For both positions, I did equilibration in NPT ensemble with following mdp file. --------------------------------------------------------------------------------------- ; Run parameters integrator = md ; leap-frog integrator nsteps = 250000 ; 2 * 500000 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstxtcout = 100 ; xtc compressed trajectory output every 2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation = no ; Restarting after NVT 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 = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; 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 ; More accurate thermostat tc-grps = CHOL_DOPC drg SOL ; three coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = semiisotropic ; uniform scaling of x-y box vectors, independent z tau_p = 5.0 ; time constant, in ps ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar) compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1 ; 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 = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --------------------------------------------------------------------------------------- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For position (a): I corrected pbc problem by trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc mol -center I selected CHOL_DOPC-drg group for centering. So problem was solved, approximately. For position (b) in which drug molecule is not in the center of lipid, I can not use -center or I can not use group containing drug molecule for centering. How to fix this problem. Any help will highly appreciated. -- 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
