[gmx-users] make hole error!!

[nanyu101]

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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