[gmx-users] Water molecule starting at atom x can not be settled - minimization step

[Trang]

Dear gmx-users,
I do a minimization run with this mdp:
-----------------------------
constraints         =  none
;define              =  -DFLEX_SPC
integrator          = cg
;nstcgsteep         = 300
emtol               =  100.0
emstep              =  0.005
dt                  =  0.001    ; ps !
nsteps              =  200000  ; total 200 ps.
nstcomm             =  100
nstxout             =  10000
nstvout             =  0
nstfout             =  0
nstlog              =  10000
nstenergy           =  1000
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
coulombtype         =  PME ; Reaction-Field
fourierspacing      =  0.12
pme_order           =  4
optimize_fft        =  yes
;epsilon_r           =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  SOL
tau_t               =  0.01    0.01
ref_t               =  310     310
; Energy monitoring
energygrps          =  Protein SOL
; Isotropic pressure coupling is now on
Pcoupl              = berendsen
Pcoupltype          = isotropic
tau_p               =  0.25
compressibility     =  5.4e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
;gen_temp            =  300.0
;gen_seed            =  749261

---------------------------
and get the error, output like this:

Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =       200000
   F-max             =  4.69437e+04 on atom 2513
   F-Norm            =  1.05294e+03


step -1: Water molecule starting at atom 43372 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

...

Fatal error:
1 particles communicated to PME node 4 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
--------------------------

I did a successful run with another equivalent system (same protein
sequence, same number of atoms), even with a LARGER TIMESTEP, 0.002 ps
I found a lot of people encounter the same error, but in production run
step. And in those cases, they're advised to minimize/equilibrate the system
more thoroughly. What can I do to resolve this problem in MINIMIZATION step?

Many thanks
Trang
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100930/64b0b01c/attachment.html>