Hi Joern,
Did you first perform an energy minimization in vacuum? The values you
get indicate severe problems with your starting structure.
By the way, for such a system you don't want to use a cubic box. It's
an utter waste of resources. You're better off with a rhombic
dodecahedron, or you can contact me off list if you want to cut your
volume by half and still have the same distance between periodic
images (right, speed up your simulations >2*).
Cheers,
Tsjerk
On 1/12/07, Joern Lenz <[EMAIL PROTECTED]> wrote:
dear users,
i try to simulate a system of DNA (17 bp) and a protein (420 aa).
before i start my MD runs, i solvated the system in a cubic box (-d = 0.9) and
started a minimization of it using the em.mdp file which you can see at the
bottom of this email.
unfortunately the minimization breaks (see below).
And if it does not break, it is very slow (20 iterations take about 3 weeks).
Can you see from the information i give to you, why this happens?
The output of this minimizations looks something like:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 400
Step= 0, Dmax= 5.0e-04 nm, Epot= 4.14463e+16 Fmax= inf, atom= 2005
Step= 1, Dmax= 5.0e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
Step= 2, Dmax= 2.5e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
Step= 3, Dmax= 1.3e-04 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
Step= 4, Dmax= 6.3e-05 nm, Epot= nan Fmax= 0.00000e+00, atom= 0
...
Hence there is an infinitive force acting on atom 2005 in my system, right ?
First I looked at the coresponding file to figure ot which residue this atom
belongs to. I then looked at the system using chimera as a viewer and found
that is residue occurs several times in my system, which worries me a little
bit. But there is no such thing like two atoms lying very close to each other
which would explain the Fmax= inf, atom= 2005 line in the minimization.
Has anyone got an idea of what is going wrong here or do you need more
information about my used files.
It would be of great help for my further work, so thanks a lot in advance and
have a nice weekend
Greetings
====================
em.mdp:
title = Minimization of blah.pdb
cpp = /usr/bin/cpp
define = -DFLEX_SPC
integrator = steep
nsteps = 400
nstenergy = 5
nstxtcout = 5
nstlist = 5
ns_type = simple
rlist = 1.0
coulombtype = PME
rcoulomb = 1.0
rvdw = 1.0
pbc = xyz
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-5
optimize_fft = yes
constraints = none
emtol = 1.0
emstep = 0.005
====================
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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