Adjusting Density of waterbox used by solvate

From: Leonardo Sepulveda Durán (
Date: Sun Jun 12 2005 - 21:51:51 CDT

Hello list!!!

I would like to perform NVE or NVT dynamics in NAMD, to prove which is
the influence of water density in my protein. I have used NPT, and I
have found that, altrough average presure is well mantained, it
fluctuates a lot, and volume too. I Thought a good way to adjust it is
to solvate the system with a waterbox that has a desired water density
from the begining. About such posibility, I would like to ask some

1) it is posible to say solvate plugin of vmd to use a diferent pdb
for initial coordinates of water which have a desired density, or use
a diferent script to allow for it,

2) if 1) is posible, does someone knows if there is a place where
waterboxes of diferent density are available to be dowloaded? or maybe
namd have it and I haven't found them??

Thanks a lot


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:50 CST