AMBER Archive (2006)

Subject: AMBER: SHAKE problem after minimization

From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Nov 22 2006 - 05:39:18 CST

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
 &cntrl
  imin = 1,
  maxcyc = 5000,
  ncyc = 2000,
  ntb = 1,
  ntr = 0,
  cut = 10
 /
--------------------------------------------------------------------------------------------------------------

-------------------------------------------------------------------------------------------------------------

res on the protein with 0.5fs timestep
 &cntrl
  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
10.0
RES 1 791
END
END

---------------------------------------------------------------------------------------------------------------------

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,

Rachel

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