Dear Amber users,
I am facing an old problem with MD -- each time I tried to restart my
simulation after minimization or initial structure the system crashes with
the message:
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 8 87 243 244
It is a rather beat up issue, but I still would like to hear some inputs. I had
this problem before, but managed to overcome it by running
minimization under different conditions to improve starting coordinates,
increasing the vlimit or dsum_tol values or lowering the temperature to
0. Also, I know that sometimes the box coordinates needed to be specified
in the input file in order to avoid this problem. This time nothing helps
and I can not even pass the first few steps. The structure looks pretty
decent and I can not find where is the problem. Well, my question is:
Is there any way to kick the structure out of this "bad" or not "acceptable"
starting conformation using MD? It has been a long time since I used
amber mail list and maybe some new suggestions/thoughts are available.
The only suggestions found from mail archive, are the one I mentioned
above....I would appreaciate any input. I am using amber 7.
thank you -- anton
***************************
* Anton B. Guliaev, Ph.D *
* Life Sciences Division *
_ * LBNL, Berkeley CA 94720 * _
/ )* abguliaev.lbl.gov *( \
/ / * F:(510)-486-6488 * \ \
_( (_ * T: 510-486-5773 * ) )_
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Received on Tue Jul 15 2003 - 22:53:01 PDT
