[gmx-users] cholesterol distortion

[Jian Dai]

Hi, all:
I got the initial structure of a DPPC bilayer from Dr. Karttunen's website,
use the parameters (hopefully) from their paper: Patra, Karttunen, Hyvönen,
Falck, Lindqvist, Vattulainen, Biophys. J. *84*, 3636-3645 (2003) to run for
100ns then replace some DPPC molecules with cholesterols, do the energy
minimization, run for 20ns and the cholesterols are distorted as shown in
the attached file.

Here are parameters for the pure DPPC run which I deem important:

nstcomm                  = 1
comm_grps                = DPPC SOL
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 1.0
coulombtype              = PME
rcoulomb                 = 1.0
vdwtype                  = Cutoff
rvdw                     = 1.0
ewald_rtol               = 1e-5
optimize_fft             = yes
tcoupl                   = Berendsen
tau_t                    = 0.1   0.1
tc_grps                  = DPPC  SOL
ref_t                    = 323   323
pcoupl                   = Berendsen
pcoupltype               = semiisotropic
tau_p                    = 1          1
compressibility          = 4.5e-5     4.5e-5
ref_p                    = 1.0        1.0
gen_vel                  = yes
gen_temp                 = 325
gen_seed                 = 173529
constraints              = all-bonds
constraint_algorithm     = LINCS
lincs_order              = 4

For the DPPC-CHOL combined system I only changed corresponding sections to:

comm_grps                = DPPC CHOL  SOL
tau_t                    = 0.1   0.1   0.1
tc_grps                  = DPPC  CHOL  SOL
ref_t                    = 323   323   323

Any suggestion is appreciated. Thank you.

Jian
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