On Wed, Jan 23, 2008, priya priya wrote:
>
> I am doing simulations at 550K using some constraints on the peptide.There
> is an error read as:
>
> vlimit exceeded for step 64; vmax = 20.6735
> vlimit exceeded for step 65; vmax = 26.7190
> vlimit exceeded for step 66; vmax = 24.7766
> vlimit exceeded for step 71; vmax = 60.0784
>
> nstlim=10000, dt=0.002,gbsa =1,surften=0.005,
It might not be possible to use a 2 fs time step at such a high temperature.
You might also try ntt=3 as a comparison. It is odd (but perhaps just a
coincindence) that the errors happen so early in the simulation--as I
understand your email, you equilibrated the system before this run, and did
not see such failures there. Be sure that you didn't change any parameters
after the equilibration step.
I'm not sure that ntt=2 would be very effective with GB: there are no
collisions with solvent to drive temperature equilibration, which is why we
generally recommend Langevin thermostats for such runs.
...dac
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jan 27 2008 - 06:07:07 PST
