[gmx-users] something wrong about making hole

[nanyu101]

Dear gmx-users,
  I have faced some mistakes in making hole in bilayer.I tried to use popc128a.pdb to make a hole for my cylinder ion channel.First  I have minimized popc128a.pdb with NVT.The system told me as follow.FIrst my energy is very below:1-1.5e5 and my force is very big:from 900 -1500.I have asked this proble to Dr.Peter Tieleman,but Dr.Tieleman said that's OK and I can make a hole without Pcoupl in it.
  When I run make_hole.pl and md_hole.The system told me as follows. There is my run.mdp below,too.
Back Off! I just backed up insert.edr to ./#insert.edr.2#
starting mdrun 'popc'
20000 steps,     40.0 ps.


Back Off! I just backed up insert.trr to ./#insert.trr.2#
step 120, will finish at Thu Feb 20 19:04:24 2003Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction at distance larger than 2.25
These are ignored for the rest of the simulation
turn on -debug for more information
Fatal error: ci = -2147483648 should be in 0 .. 2534 [FILE nsgrid.c, LINE 210]


cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	; ps !
nsteps              =  20000	; total 10 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  10
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
pme_order           =  4
fourierspacing      = 0.12
optimize_fft        = yes
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
Pcoupl              =  no
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps		    =  POPC	SOL
tau_t               =  0.1	0.1
ref_t               =  300	300
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529


I hope you can give me a suggest about.

Thanks a lot.

Best wishes,
Xianhui Wu


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