[gmx-users] make hole error!!
nanyu101
nanyu101 at sina.com
Wed Feb 19 03:04:39 CET 2003
Dear gmx-users,
I have tried to make a hole in DPPC bilayer.My operations as follows:
1.make the hole by hand or with make_hole.pl
2.grompp -f run.mdp -o insert.tpr -c dppc114.pdb -r dppc114.pdb -p dppc.top
3.mdrun -v -hole -holep hb.mdp -deffnm insert
The following information was informed by system.My mdp file followed the information.
starting mdrun 'bilayer'
5000 steps, 5.0 ps.
step 350, will finish at Tue Feb 18 18:06:38 2003Warning: 1-4 interaction at distance larger than 1
These are ignored for the rest of the simulation
turn on -debug for more information
step 360, will finish at Tue Feb 18 18:06:43 2003
Step 361 Warning: pressure scaling more than 1%, mu: 1.06386 1.06386 1.06386
Step 362 Warning: pressure scaling more than 1%, mu: 4554.19 4554.19 4554.19
Step 363 Warning: pressure scaling more than 1%, mu: 1.54073e+07 1.54073e+07 1.54073e+07
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported.
Box (3x3):
Box[ 0]={ nan, nan, nan}
Box[ 1]={ nan, nan, nan}
Box[ 2]={ nan, nan, nan}
Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
md.mdp
;
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = /lib/cpp
define = -DPOSRES
constraints = none
integrator = md
emtol = 100
emstep = 0.01
nsteps = 5000
nstcgsteep = 1000
pbc = xyz
nstxout = 500
nstvout = 500
nstlog = 500
nstlist = 10
ns_type = grid
rlist = 0.8
rcoulomb = 1.4
rvdw = 0.8
tcoupl = no
Pcoupl = Berendsen
tau_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
gen_vel = yes
gen_temp = 100
gen_seed = 173529
constraint-algorithm = SHAKE
shake_tol = 0.0001
hb.mdp
holetype = Cyl
hfm = 10
supf = 20
molsurf_log = gsurf.log
hr = 1.0813
hx = 2.7
hy = 2.8
hz = 5.0
hp1 = 1
hp2 = 6654
s1 = 6655
s2 = 25961
hz1 = 3.3
hz2 = 7.3
sfm = 10.0
sofs = 0.15
molsurf_file =
debugsurf = yes
resforces = yes
Thanks.
Best wishes,
Xianhui Wu
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