re: shake/potential function

From: Bill Ross <>
Date: Thu 2 Nov 2000 10:21:26 -0800 (PST)

        I'm trying to simulate a very large molecule. For this reason I'm doing a
        vacuum simulation and I use shake on all bonds (ntc = 3 with ntf = 3)
        in order to save as much computational time as possible. (Larger
        timestep...) But I get the following message:

             NITER, NIT, LL, I AND J ARE : 0 11 4973 3178 3180

        What does this mean?

SHAKE has failed. It would be of interest to see what
the temperature was. Try more gradual warming, and first
get things moving at 10K with ntc=ntf=2. And see the amber
web Questions sections on equilibration and blowup.

          dt = 0.001,
         type='TEMP0', istep1=0, istep2=2000,
         value1=0.0, value2=50.0,
         type='TEMP0', istep1=2001, istep2=5000
         value1=50.0, value2=300.0,

         type='TEMP0', istep1=5001, istep2=10000
         value1=300.0, value2=300.0,

(The last stage isn't needed - temp remains fixed at the
final value of the end of the previous stage.)

Bill Ross
Received on Thu Nov 02 2000 - 10:21:26 PST
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