AMBER Archive (2003)

Subject: AMBER: 1 fs timestep for GB?

From: Peter VARNAI (Peter.Varnai_at_ibpc.fr)
Date: Tue Nov 25 2003 - 11:48:35 CST

Dear All,

I noticed that people tend to use 1 fs time-step for integration in GB/SA
simulations. I understand that the scheme implemented does not involve
friction with the environment and this can give rise to faster
motions in some degrees of freedom of the solute. I am not sure how much
faster bonds fluctuate in this case, but a 2 fs integration step
did not produce anything strange for my nucleic acid simulation:
no drift in total energy over 10 ns - although the simulation was
run at constant temperature (300 K) with tautp=5.0.

Any experience on this or comment is apperciated.

Peter Varnai

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu