[gmx-users] correct traj for water/ions density

Justin Lemkul jalemkul at vt.edu
Mon May 6 14:02:59 CEST 2013

On 5/6/13 7:32 AM, gromacs query wrote:
> Dear Justin,
>>> You don't need to change the trajectory in any way to do density
> measurements
> I read sometime before in some paper: water density falls around polymer
> (COM) at a distance nearly 4.5nm when it is in box of 10x10x10 nm. I assume
> the polymer must be near the center of box so 5nm on either sides.
> Then in my case (polymer at the box edge) how the box size will be
> considered. I mean to say if my box is 10x10x10 and I calculate density it
> will never fall around 5nm distance from polymer as my polymer is at edge
> and will give different pattern.

Now the statement of your problem is more clear.  To calculate the density 
within the box, you do not need to do any manipulation.  For your purpose, where 
a fixed reference is convenient, there's certainly nothing wrong with centering 
the polymer.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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