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

[David van der Spoel]

Mahnam wrote:
> 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.
> 
did you use constraints?
you probably want to use
constraints = all-bonds
read manual chapter 1.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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