I would also add that the settings provided below probably produce severe cutoff
artifacts. In my experience, the only stable settings are those of the
all-vs-all kernel (with infinite cutoffs).
-Justin
Per Larsson wrote:
Hi
There has been a number of reports lately about ill-behaving simulations using
implicit solvent. I'm currently trying to investigate the cause of this, as
such simulations used to work very nice in our hands.
In the meantime I would advice to use implicit solvent with caution.
Thanks
/Per
Skickat från min iPhone
30 okt 2011 kl. 02:10 skrev Matt Larson <larsonma...@gmail.com>:
I've been having problems getting implicit solvent systems (which are
probably fairly experiment still in gromacs) to work correctly. I've
been modelling a protein of about 11000 atoms with hydrogens in a 2 ns
simulation. By the end of the simulation, the temperature has risen
from 300 K to 496 K - and the protein unfolds. It was supposed to
maintain temp at 300 K.
I have an a non-zero total charge of -6.999999. With explicit
solvent, I would normally add the appropriate matching ions, but with
implicit solvent what should you do? Could the non-zero total charge
result in heating? Or is the thermostat not working well enough
(should I change tau-t or ref-t?)
Here is my md.mdp file:
constraints = all-bonds ; trying..
integrator = md
dt = 0.002 ; ps !
nsteps = 1000000
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = cut-off
fourierspacing = 0.16
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 1.0 ; important for neighbor searching
pbc = no ; no periodic boundary conditions
epsilon_rf = 0
rgbradii = 1.0 ; must equal rlist, rcoulomb, rvdw
comm_mode = angular
optimize_fft = yes
implicit_solvent = GBSA
gb_algorithm = OBC
gb_epsilon_solvent = 80
sa_surface_tension = 2.25936
nstcomm = 10
nstxout = 1000
nstxtcout = 1000
nstvout = 0
nstfout = 0
tcoupl = andersen
tc-grps = system
tau-t = 0.1
ref-t = 300
gen_vel = yes
gen_temp = 300
gen_seed = -1
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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