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
