Trang wrote:
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?
You likely have some unresolvable atomic clash(es) in your system that can't be
energy-minimized. Check your structure around the location of the problematic
water molecule to see if anything is overlapping.
-Justin
Many thanks
Trang
--
========================================
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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