5Hello all, I am trying to use CHARMM 36 for DPPC membrane simulation. I did the following so far:
1. Download pdb file containing 128 DPPC molecules from http://www.charmm-gui.org/?doc=archive&lib=lipid_pure 2. I separated one lipid molecule from the obtained pdb file and used pdb2gmx -f 1dppc.gro -nochargegrp The top file obtained was converted to itp file by commenting few things out. 3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer from CHARMM GUI for the box length. I used editconf to convert the pdb to gro and manually inserted the box size in the gro file. 4. Created a system.top file which looks like #include "charmm36.ff/forcefield.itp" #include "lipid.itp" #include "charmm36.ff/tips3p.itp" [ system ] chol [ molecules ] DPPC 128 SOL 3659 5. I used following mdp settings integrator = md ; leap-frog integrator nsteps = 20000000 ; 40 ns dt = 0.002 ; 2 fs ; Output control nstxout = 100000 ; save coordinates every 200 ps nstvout = 100000 ; save velocities every 200 ps nstenergy = 10000 ; save energies every 2 ps nstlog = 10000 ; update log file every 2 ps ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 10 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rlistlong = 1.4 vdwtype = switch rvdw = 1.2 ; short-range van der Waals cutoff (in nm) rvdw_switch = 0.8 ; Electrostatics rcoulomb = 1.0 rcoulomb_switch = 0.0 coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 6 ; cubic interpolation fourierspacing = 0.15 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; More accurate thermostat tc-grps = DPPC SOL ; two coupling groups - more accurate tau_t = 0.2 0.2 ; time constant, in ps ref_t = 323.15 323.15 ; 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 = No ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes gen_temp = 200.0 gen_seed = 173529 ; COM motion removal nstcomm = 1 comm-mode = Linear comm-grps = DPPC SOL ; Energy monitoring energygrps = DPPC SOL ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy The resulting simulation gave me an area per lipid =0.591 nm^2. This is not quite right. Can somebody suggest what else could i do it get close to the 0.63 nm^2 value. Also when i looked at trajectory file it seemed that the box length was not set up quite right because the downloaded pdb file looked ok with the membrane in the middle but at the next frame the membrane was at a totally different location. The leaflets were separated and the middle of the membrane was at the edge of the box. Also when i used pdb2gmx -nochargegrp on the downloaded file it created a gro file whose system size was 8.20170 8.64120 6.54740 in contrast to 6.40000 6.40000 6.38452 . Amit
-- 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