[gmx-users] seperating bilayers (again)

[Alan Dodd]

Hello all,
I've been having some trouble recently with the
leaflets in my bilayer gently drifting apart over a
period of a few hundred picoseconds.  Increasing the
vdW radius hasn't helped (up to 2nm), although it did
delay the seperation.  Likewise, increasing tau_p from
5 up to 10.  The really bizarre thing is that I've
been simulating peptides in bilayers using 3.2.1 on
our cluster for about 18 months now, using the
lipid-modified version of ffgmx and the parameters
listed below, and it's only since I've started using
3.3 on a new machine that I've had any trouble.  Any
suggestions on what might be going wrong?

title               =  Yo
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.0015   ; ps !
nsteps              =  5000000  ; total 7500 ps.
nstcomm             =  1
nstxout             =  1000
nstvout             =  1000
nstfout             =  0
nstlog              =  1000
nstenergy           =  1000
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  1.5
rcoulomb            =  1.5
rvdw                =  1.5
pme_order           =  8
fourierspacing      =  0.2
optimize_fft        =  yes
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  DOPC     SOL  Protein      Cl
tau_t               =  0.1      0.1      0.1     0.1
ref_t               =  300      300      300     300
; Energy monitoring
energygrps          =  DOPC     SOL  Protein
; Isotropic pressure coupling is now on
Pcoupl              = berendsen
Pcoupltype          = surface-tension
tau_p               =  5
compressibility     =  4.5e-5 4.5e-5
ref_p               =  410 1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


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