Center on a particular lipid? Or head group? Mark On Oct 23, 2013 6:13 PM, "shahab shariati" <shahab.shari...@gmail.com> wrote:
> 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? 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