huifang liu wrote:
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:
Your system is exploding. Have a look here:
http://wiki.gromacs.org/index.php/Errors#1-4_interaction_not_within_cut-off
as well as:
http://wiki.gromacs.org/index.php/blowing_up
-Justin
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
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--
Justin A. Lemkul
Graduate Research Assistant
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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