# Re: AMBER: Question about NVE simulation.

From: Carlos Simmerling <carlos.simmerling.stonybrook.edu>
Date: Tue, 18 Oct 2005 16:23:02 -0400

the initial velocities determine the kinetic energy, and the potential
energy is dependent on the structure. so you're right, the sum of those
will depend on what kinetic energy it has. different sets of velocities
will differ slightly, and SHAKE will change things too. I think most people
do short equilibration at NVT and then switch to NVE. For example,
if you take your minimized structure and run at NVE without equilibration,
you will end up at a much lower T than your initial assignment (due
to SHAKE and also quite a bit of the kinetic energy going into potential
energyt for the thermal fluctuations).

Chunhu Tan wrote:

> Dear Carlos,
> 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 - 21:53:01 PDT
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