Hi Franz,
One cause of this that I've encountered is dihedral angle restraints
that have force constants that are too large. The cdih force constant is
the product of an overall weight factor S ("scale") set in the annealing
script, and an energy constant C set in the dihedral angle restraint
file. If the product of S and C is accidentally large, sa.inp can "blow up".
Even with the internal variable engine, large dihedral angle restraint
force constants can cause problems. In that case, the time step will
keep halving until it is too small, and the run will abort.
Keith
John Kuszewski wrote:
Hi Franz,
This is a fairly common problem using the 'classic' xplor dynamics
engine. It can be caused by
several things:
1. Bad covalent restraints (bonds, angles, etc), caused by bad
parameter sets. If you're using the
current protein.par and protein.top files, that's probably not the
issue.
2. Bad distance restraints (and to a much lesser extent, bad
covalent restraints). In this context,
'bad' could mean too tight a distance range, too high a force
constant, or inconsistent with each other.
3. Bad luck. Try running with a different random number seed.
Of these, the most common problem is distance restraints that are too
tight or inconsistent with each other.
Particularly if your temperature explosions are occurring at the
beginning of the cooling phase,
because that's when full vdW restraints are added in, and so some
distance restraints that could
be satisfied by coordinates that included vdW overlap suddenly start
fighting with the vdW term.
N.B. If you're using Charles's internal variable dynamics engine, you
can set it to avoid this problem
a lot of the time by allowing it to take variable-sized timesteps.
That prevents the simulation from
injecting extra energy into the system in regions where the potential
energy surface is changing
steeply.
Hope this helps.
JK
On Nov 27, 2007, at 1:48 PM, Franz Hagn wrote:
Hi all,
during the xplor calculation (with sa.inp script and xplor 2.16),
after
high temperature dynamics, I get unusual high temperature and abortion
of the run. Does anybody know some hints? Are my restraints to
rigorous ?
Thanks, Franz
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