AMBER Archive (2003)

Subject: non-periodic system

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Wed May 21 2003 - 17:50:18 CDT

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