non-periodic system

From: Ioana Cozmuta <ioana.nas.nasa.gov>
Date: Wed, 21 May 2003 15:50:18 -0700 (PDT)

Hi amber users,

I know this is maybe a naive question but I was wondering if one has a
non-periodic system (say a solvated protein) what is the best way to
equilibrate the system at the right density?
Normally one would use NPT dynamics and the strange thing is that I can
use NPT dynamics for a non-periodic system in NAMD without getting any
error. So I was wondering what is the way to do NPT for a non-periodic
system. What are the approximations involved?

Anyone's suggestions/comments would be welcomed?

Thanks,
Ioana
Received on Thu May 22 2003 - 00:53:00 PDT
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