[gmx-users] OPLS/AA + TIP5P, anybody?
gigo at ibb.waw.pl
Tue Oct 1 11:02:17 CEST 2013
By now 7ns of the MD passed without a single warning.
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
> 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
> empty gro file (http://shroom.ibb.waw.pl/tip5p/pure2). I understand
> 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
> 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
> 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?
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