AMBER Archive (2006)

Subject: RE: AMBER: SHAKE problem after minimization

From: Ross Walker (
Date: Wed Nov 22 2006 - 11:59:58 CST

Dear Rachel,
Seeing shake failure is a function of deeper problems with your system and
is not an issue with using shake. If you turn off shake and run the
simulation your simulation will run for longer and then die.
The issue is most likely that you have a very bad/strained starting
structure that minimization could not clean up. Unfortunately you don't give
the energies for the first step of your MD or from the end of your
minimization so it is hard to see where the problem is coming from. Often
though these problems arise because you have 2 atoms sitting on top of each
You can try the check command in leap. You should also look at your
minimisation and see which atom has the largest force on it - printed on the
NSTEP line. This will give you a clue where to look. You can also, if you
want to see what is going wrong, set the time step very short, say 0.1fs
(dt=0.0001) and also set ntwx=1 and turn off shake. Then run for about 50
steps or so and then open the trajectory file in a viewer such as vmd and
you should be able to watch your system blowing up and see from where the
problem originates.
All the best

|\oss Walker

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From: [] On Behalf Of
Sent: Wednesday, November 22, 2006 03:39
To: amber
Subject: AMBER: SHAKE problem after minimization

Dear all,
I have a problme with SHAKE after minimization, when I started to run md,
this is the error message i got:

     Coordinate resetting (SHAKE) was not accomplished
     within 3000 iterations

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

And the following are the scripts i used to run minimization and md:


initial minimisation whole system
  imin = 1,
  maxcyc = 5000,
  ncyc = 2000,
  ntb = 1,
  ntr = 0,
  cut = 10


res on the protein with 0.5fs timestep
  imin = 0,
  irest = 0,
  ntx = 1,
  ntb = 1,
  cut = 10,
  ntr = 1,
  ntc = 2,
  ntf = 2,
  tempi = 0.0,
  temp0 = 300.0,
  ntt = 3,
  gamma_ln = 1.0,
  nstlim = 30000, dt = 0.0005,
  ntpr = 100, ntwx = 100, ntwr = 500
Keep the protein fixed with weak restraints
RES 1 791


I have tried to use even smaller timestep such as 0.3fs or even 0.1fs, but
still i had same problem, and when i used very small timestep such as 0.1fs,
i will have error messages ' vlimit exceeded for step 1 ; vmax =
76.6082699232639' as well before it complained about the SHAKE problem.

Can anyone suggest what might be the causes of this SHAKE failure please?
thanks a lot in advance!

Best regards,


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