On Mon, May 17, 2004, Venkata S Koppuravuri wrote:
>
> I am trying to do a Simulated annealing on a protein structure and I got
> the following error.
> --------------------------
> vlimit exceeded for step 0 ; vmax = 25661.90229977621
> vlimit exceeded for step 1 ; vmax = 271.9070745233018
> vlimit exceeded for step 2 ; vmax = 11.03999138171793
> vlimit exceeded for step 3 ; vmax = 6.104038534855053
> vlimit exceeded for step 4 ; vmax = 6.405817372735854
> ....
> ....
> --------------------------
>
> I have protonated the structure but have not hydrated it. Below is the
> script that i have used.
>
> -------------
> &cntrl
> nstlim=20000, pencut=-0.001, nmropt=1,
> ntpr=200, ntt=1, ntwx=200,
> cut=15.0, ntb=0, vlimit=5,
> lastist = 7500000, lastrst = 7500000,
> /
Just a general note to add to Carlos' reply: when you are starting a new
system, don't begin with nstlim=20000 and ntpr=200. Start with nstlim=10
and ntpr=1, and study the output carefully for clues about whether the
initial energy is OK, and so on, and whether the system is doing what you
want. It's also generally a good idea to do an intial minimization (again,
start with a short run and set ntpr=1) to ensure that the starting coordinates
make sense.
....good luck...dac
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Received on Mon May 17 2004 - 20:53:01 PDT
