[gmx-users] Problems with molecular dynamic investigation of an cyclic peptide nanotube

[huifang liu]

Hi, Gromacs users,

I was caught by a big problem with molecular dynamic investigation of an
cyclic peptide nanotube. When i do energy minimization with em.mdp parameter
file as follows, it gave out a warning: Warning: 1-4 interaction between 135
and 144 at distance larger than 1 nm. I ignored it and went on the next step
with pr.mdp as follows, but it crashed with the following information:


Wrote pdb files with previous and current coordinates

[node1:15777] *** Process received signal ***

[node1:15777] Signal: Segmentation fault (11)

[node1:15777] Signal code: Address not mapped (1)

[node1:15777] Failing at address: 0xba8e28

[node1:15777] [ 0] /lib64/tls/libpthread.so.0 [0x3078e0c5b0]

[node1:15777] [ 1] mdrun_ompi(inl3100+0x248) [0x524b58]

[node1:15777] [ 2] mdrun_ompi(do_fnbf+0xfe7) [0x4a3d97]

[node1:15777] [ 3] mdrun_ompi(force+0x120) [0x4432f0]

[node1:15777] [ 4] mdrun_ompi(do_force+0xb8b) [0x471afb]

[node1:15777] [ 5] mdrun_ompi(do_md+0x139f) [0x426fdf]

[node1:15777] [ 6] mdrun_ompi(mdrunner+0xb9c) [0x42a6dc]

[node1:15777] [ 7] mdrun_ompi(main+0x1dd) [0x42aabd]

[node1:15777] [ 8] /lib64/tls/libc.so.6(__libc_start_main+0xdb)
[0x307851c3fb]

[node1:15777] [ 9] mdrun_ompi [0x412e8a]

[node1:15777] *** End of error message ***

Segmentation fault



I am extremely puzzed and don't know how to solve this problem. In additon,
my previous system runs normally with the same parameter file.



##############em.mdp file

cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  steep
nsteps              =  100
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no







#########pr.mdp

title               =  Yo
cpp                 =  /lib/cpp
define              =  -DPOSRES
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  2500  ; total 5 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  1000
nstfout             =  0
nstlog              =  500
nstenergy           =  500
nstlist             =  5
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
pme_order           =  4
optimize_fft        =  yes
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =   Protein
tau_t               =   0.1
ref_t               =    10
; Energy monitoring
energygrps          =  Protein
; Pressure coupling is not on
Pcoupl              =  berendsen
pcoupltype          =  anisotropic
tau_p               =  1
compressibility     =  4.5e-5 4.5e-5 4.5e-5 0 0 0
ref_p               =  1 1 1 1 1 1
; Generate velocites is on at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529





Look forward to your help. Thanks in advance.



Huifang
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080903/c89bd822/attachment.html>