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

Christopher Neale chris.neale at alum.utoronto.ca
Thu Feb 9 05:07:08 CET 2017

5 ns is not long enough to equilibrate the APL, and it's a time-averaged property in experiment, so looking at one frame is not as good as averaging over tens of ns of simulation. Try running for 100 ns and taking the average of the last 50 ns. Also, what APL do you get and what value do you consider correct? Also look at the time-series of the APL to see if it is drifting in the right direction. I presume that you're computing APL as box_x * box_y / N lipids per leaflet (the per leaflet part obviously being important).

I think Tieleman was using a 0.9 nm LJ cutoff the last time he was working with the Berger lipids. Your 1.4 nm LJ cutoff is sure to decrease the APL in comparison to that.

Finally, not all parameters give APL values that agree with experiment, so check the literature on your parameters (and cutoff) to see if at least you are getting something similar to what other people get.

Other than the LJ cutoff, which is not necessarily wrong but at least could lead to differences, your mdp file looked fine to me.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of ali.khourshaei71 at student.sharif.edu <ali.khourshaei71 at student.sharif.edu>
Sent: 08 February 2017 18:51:11
To: gmx-users at gromacs.org
Subject: [gmx-users] Problem with obtaining rational Area per lipid

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

Eagerly looking forward to hear back from you.





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 ;


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)
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
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