Dear Chris,
By now 7ns of the MD passed without a single warning.
Best Regards,
Grzegorz
P.s. The mdp:
constraints = none
integrator = md
dt = 0.001 ; ps
nsteps = 10000000 ; total 10 ns
nstcomm = 1000
nstxout = 0
nstvout = 0
nstfout = 0
nstxtcout = 25
xtc_grps = System
nstlog = 1000
nstenergy = 1000
nstlist = 20
ns_type = grid
rlist = 1.3
coulombtype = PME
fourierspacing = 0.1
pme_order = 4
optimize_fft = yes
rcoulomb = 1.3
rvdw = 1.3
vdwtype = cut-off
pbc = xyz
DispCorr = EnerPres
Tcoupl = v-rescale
ld_seed = -1
tc-grps = System
tau_t = 0.1
ref_t = 300.0
pcoupl = Parrinello-Rahman
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
gen_vel = no
cutoff-scheme = Verlet
On 2013-09-30 21:47, Christopher Neale wrote:
One a system passes EM and a couple of ps of MD, is it always stable
indefinitely? If not, then
something is wrong somewhere.
-- original message --
Dear Chris,
I put one tip5p molecule in a center of dodecahedral box - 2nm from
that
molecule to walls, filled it with tip5p, ran 6000 steps of steep
minimization. After another 2704 steps of cg it converged to emtol 1.0.
I run 100k steps of nvt on this box afterwards
(http://shroom.ibb.waw.pl/tip5p/pure1). But the water is very
capricious. If I ran only 2000 steps of steep, the following cg crashed
after less than 1000 steps because a water molecule could not be
settled. I could not minimize another box, filled only by genbox from
an
empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand
that
you have to have some luck if you run a simulation in pbc with rigid
water, which interacts through walls of the box with the other side and
was not well placed. Also, I had several segfaults during minimization
that I was able to avoid only by limiting the number of cores.
I checked distances between OW and LPx on a crashing minimization with
a
peptide - 2812 water molecules. Maximum force reached 8.8e+24 in 225
steep steps, but all the 5624 distances were rock solid 0.7A, as
expected.
I still did not post the redmine issue, I want to be sure that I am
doing everything correctly.
On 2013-09-29 18:47, Christopher Neale wrote:
Dear Grzegorz:
Under no conditions should any of the tip5p geometry change (for the
standard tip5p model).
If you find that this is happening, then that is certainly an error.
You can check if you like by analyzing
your trajectory. However, flexible bonds will allow the distance from
the arginine N to the arginine
H to vary, which my allow a closer approach of the arginine H to the
tip5p dummy site.
Did you verify that a water box (no protein) simulates without error?
Did you post a redmine issue with .mdp , .gro , and .top files?
Chris.
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