Hi Everyone, I did another simulation where i found the the DPPC area per lipid is 0.61 nm^2 . Is this acceptable ?
I have seen issues like this on the mailing list before can one of the experts give me some hints. Amit On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey <kgp.a...@gmail.com> wrote: > > 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 >
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