What is your van der Waals cut-off distance? From our experience
years ago, we sometimes saw this if our van der Waals cut-off was too
short; i.e., less than 15 angstroms. That seems long, since it falls
off as sixth power, but because the long-range van der Waals is all
attractive, there is no shielding (unlike the electrostatic force).
At 11:03 AM 4/6/2006, you wrote:
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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---------------------------------
Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
3261 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896 fax 217-244-2909
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