AMBER Archive (2004)

Subject: AMBER: Amber8: Vlimit problem again

From: Yuhui Cheng (
Date: Thu Jul 15 2004 - 21:34:58 CDT

Hi, Everyone,
     I met the similar "vlimit exceed" problem as
posted on this forum when running MD simulation on a
protein-prduct peptide complex. The error message
shows like this from the beginning:
" vlimit exceeded for step 25175 ; vmax =

     Coordinate resetting (SHAKE) cannot be
     deviation is too large
     NITER, NIT, LL, I and J are : 0 1 2893 5813

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system."
     The value of vmax is too high(default
vlimit=20.0) to believe it. As Prof. Thomas E.
Cheatham, III replied, (1) strong overlap of atoms or
vibrational frequencies that are faster than the
integrator can handle can bring such a problem.
However, the repeated atoms I, J in the product
peptide were not noticed overlap and formed a stable
hydrogen bonding with another residue.
     Is it reasonable to increase vlmit to 90.0? Since
 my model is the product complex, is it possible to
initiate such a problem due to instability?
     My input file is as belows:
" &cntrl
  imin = 0, ntx = 7, irest = 1,
  ntpr = 100, ntwx = 500, ntwe = 0, ntwprt=0,
  ntc = 2, ntf = 2, lastrst = 3000000,
  nstlim = 50000, dt =0.002,
  tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
  ntb = 1, ntp = 0, taup = 2.0, pres0 =1.0,


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