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

[Mahnam]

In God We Trust
Hello Dear Dr David van der Spoel
Thank you for your quick response. I  had used constraints before md 
simulation. 
I have done energy minimization and position restraint (20ps) (with 
constraints=all bonds )and then md simulation at 100 K, 200K and 300K for 
100ps (with constraint=none) and then I extended my simulation at 300K for 
700ps (e.g. 1000ps md simulation)  with time step 1fs and everything is ok, 
only if I change time step to 2fs, it crashes.
 
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/



-----Original Message-----
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Sun, 15 Jul 2007 14:07:35 +0200
Subject: Re: [gmx-users] Segmentation fault after dt=2fs

> 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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