[gmx-users] Segmentation fault after dt=2fs

Mahnam mahnam at ibb.ut.ac.ir
Sun Jul 15 13:55:52 CEST 2007


In God We Trust
Hello Dear gmx-users
I  performed MD simulation on Alcohol dehydrogenase for 1ns with time step
1fs and everything was ok.Becase of very slow speed of simulation I
decided to increase the time step , then I took final structures (final gro
and toplogy files) of this simulation and run another simulation with time
step 2fs and the same parameters ,but after 109 ps I encounter with 
Segmentation fault ,even if I increase table-extention ,the result was the
same. Here is my mdp file. 

title               =  n.pdb restraining
warnings            =  10
cpp                 =  /lib/cpp
constraints         =  none
integrator          =  md 
dt                  =  0.002
nsteps              =  4850000
comm_mode           =  Linear
nstcomm             =  1
comm_grps           =  protein
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  10
nstenergy           =  250
nstlist             =  10
ns_type             =  grid
rlist               =  1.2
coulombtype         =  PME
rcoulomb            =  1.2
rvdw                =  1.4
fourierspacing      =  0.12
fourier_nx          =  0
fourier_ny          =  0
fourier_nz          =  0
pme_order           =  4
ewald_rtol          =  1e-5
optimize_fft        =  yes
table-extension     =  2
; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tau_t               =  0.1       0.1     0.1  
tc-grps		    =  protein   SOL     CL-    
ref_t               =  300       300     300   
; Pressure coupling is  on
Pcoupl              =  berendsen 
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529
 

Would you please tell me what is wrong.

Many thanks in advance for your help and your reply.
Yours truly 
Karim Mahnam
Institute of  Biochemistry  and  Biophysics (IBB)
Tehran University 
P.O.box 13145-1384
Tehran 
Iran 
http://www.ibb.ut.ac.ir/






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