[gmx-users] OPLS/AA + TIP5P, anybody?

[gigo]

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.