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 <[EMAIL PROTECTED]>
To: Discussion list for GROMACS users <[email protected]>
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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_______________________________________________
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Please search the archive at http://www.gromacs.org/search before posting!
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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