Hi Y,
That problem is very usual. I think that your problem is you are working
with the highest value for dt using shake. If shake does not respond well
so dt has to get smaller. If I were you I put a smaller value for dt and a
higher for nstlim in order to have the same simulationīs total time.
Good Luck!
G.
At 07:34 p.m. 15/07/2004 -0700, you wrote:
>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 - 14:53:00 PDT
