From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Fri Feb 10 2006 - 12:40:50 CST
if you visualize the periodic box in the original size and place, the
difference should not be that dramatic. you probably have plotted the
positions without conversions to within the periodic box. also, the
size of the periodic box should change in order to maintain P and T.
On Feb 10, 2006, at 11:58 AM, snoze pa wrote:
> Dear NAMD community,
> I am doing my simulatin at NPT. My simulation is going fine till
> heating. ut for Free MD simulation My water box size is increasing in
> one direction. While the postion of the protein remain same. I don't
> know what is wrong with this? I am also attaching after 1ns simulation
> protein and waterbox snapshot.Here are two snapshot
> 1. namdmin.png for after minimization
> 2. namd1ns.png is after 1ns free run.
> I don't know why my water box size is increasing in one direction.
> thanks in advance
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