AMBER Archive (2003)

Subject: AMBER: Coordinate resetting (SHAKE) cannot be accomplished

From: Anton B. Guliaev (anton_at_vostok.lbl.gov)
Date: Tue Jul 15 2003 - 16:35:59 CDT


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_at_lbl.gov *( \
    / / * F:(510)-486-6488 * \ \
  _( (_ * T: 510-486-5773 * ) )_
 (((\ \)**/ )*****************( \**(/ /)))
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