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

[David van der Spoel]

Mahnam wrote:
> 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.

i've already answered this one. please don't send the same question 
twice. all this is in the manual.

> 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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> 
> 
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-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++