AMBER Archive (2004)

Subject: Re: AMBER: Lennard-Jones particle simulation

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Aug 25 2004 - 15:06:47 CDT

maybe it wants to evaporate? after all, helium etc are vapor at 300K/1atm.

Thomas E. Cheatham, III wrote:

>>Can anyone suggest me a good way to equilibrate a box of Lennard-Jones
>>particles at 300K and 1atm starting with certain lattice conformation? I
>>tried minimization and a long NVT MD. But as long as I switched to NPT,
>>the system just blew up after some picoseconds. Thanks.
>>
>>
>
>Maybe the lattice conformation is not stable under NPT, i.e. that at 300K
>it wants to melt. You have to be careful to have a good balance with the
>LJ particles. I would suggest either increasing the well depth or running
>at higher pressure with a long relaxation time. You could also try
>running the lattice in vacuum to see if it still falls apart (my guess is
>that it will). It seems unlikely to be an artifact of the pressure
>coupling.
>
>
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