problem with water

From: Swarna M Patra (
Date: Tue Aug 24 2010 - 11:26:45 CDT

Hi Namd users
I am running a protein+lipid bilayer +water simulation (NVT) at zero temp..
After minimization, the protein has restrain of 500 kcal and water from one
side is vanishing and adding to the other side . I am using wralpAll option.
cutoff is 10 and pairlist is 12.5 and switch dist is 8.5. when I look into
the water molecules i see patches of hole(no water). pl help me , what
could be the possible reason and which parameter i need to adjust.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:27 CST