[gmx-users] Problem with obtaining rational Area per lipid

[ali.khourshaei71 at student.sharif.edu]

Dear Gromacs users, 

As part of my M.Sc. thesis I should do MD simulation. For this purpose,
at first I intended to regenerate a rational Area per lipid with good
agreement with experiment as verification of my subsequent MD
simulations. I downloaded the initial .pdb file from Dr. tieleman lab
website, Did a minimization and an Equilibration step. But, my final
configuration failed to give a good Area per lipid. I wonder if you
could have a very quick look on my .mdp files which is attached here and
give some short comments on it.  Also, it will be an asset for me it you
could be able to share your .mdp file in minimization and equilibration
stage with me regarding one of your published journal paper on lipid
bilayer 

Eagerly looking forward to hear back from you. 

Sincerely, 

Ali 

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Min.mdp 

integrator = steep ; 
emtol = 1000.0 ; 
emstep = 0.01 ; 
nsteps = 500 ; 

nstlist = 1 ; 
coulombtype = PME ; 
ns_type = grid ; 

rcoulomb = 1.0 ; 
rvdw = 1.4 ; 
pbc = xyz ; 

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NPT. mdp 

integrator = md ; leap-frog integrator
nsteps = 2500000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs 

nstxout = 0 ; save coordinates every 0.2 ps
nstvout = 0 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps 

continuation = no ;
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 

ns-type = grid ; search neighboring grid cels
nstlist = 10 ; 

rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm) 

coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme-order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT 

tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = DPPC 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 

Pcoupl = Berendsen
pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
independent z
tau-p = 0.25 0.25
compressibility = 4.5e-5 4.5e-5 
ref-p = 1.0 1.0 

pbc = xyz ; 3-D PBC 

gen-vel = yes ; assign velocities from Maxwell distribution
gen-temp = 323 ; temperature for Maxwell distribution
gen-seed = -1 ; generate a random seed 

nstcomm = 1
comm-mode = Linear
comm-grps = DPPC SOL