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 =
88.8293391220360
Coordinate resetting (SHAKE) cannot be
accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 1 2893 5813
5814
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
(2)
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,
&end"
Thanks,
Yuhui
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Received on Fri Jul 16 2004 - 03:53:00 PDT
