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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