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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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