Dear Carlos,
Thanks for your reply!
I am still confused about the NVE. Now I turn off SHAKE, and then
"force" Sander setting new random velocities every, say, 100 steps (with
the same TEMP0), in a ntt = 0 run. Then I find that the system will be on
defferent Etot level after each resetting of velocity. It looks like that
the Etot of system depends on the initial velocity in a NVE simulation. Is
that normal?
Best,
Chuck
----- Original Message -----
From: "Carlos Simmerling" <carlos.ilion.bio.sunysb.edu>
To: <amber.scripps.edu>
Sent: Tuesday, October 18, 2005 5:02 AM
Subject: Re: AMBER: Question about NVE simulation.
> you assigned it random initial velocities, and some of them are along the
> vectors that you constrain with SHAKE, which will remove it.
> When you use ntf=2 you tell sander not to calculate those
> energies. Try ntf=1 and see if the energy of the bonds changes.
>
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Received on Tue Oct 18 2005 - 20:53:01 PDT
