[gmx-users] Segmentation fault after dt=2fs
David van der Spoel
spoel at xray.bmc.uu.se
Sun Jul 15 16:55:57 CEST 2007
> In God We Trust
> Hello Dear Dr David van der Spoel
> Thank you for your quick response. I had used constraints before md
> 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
> -----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
>>> 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
>>> 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 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
>> gmx-users mailing list gmx-users at gromacs.org
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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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