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

gromacs query gromacsquery at gmail.com
Mon May 6 13:32:44 CEST 2013

Dear Justin,

>> You don't need to change the trajectory in any way to do density

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.


On Mon, May 6, 2013 at 1:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 5/6/13 4:21 AM, gromacs query wrote:
>> Dear All,
>> I want to calculate water and ions density around polymer. After MD I see
>> my polymer goes near the edges of box and rather some part is out of box.
>> So in order to calculate water and ion density I think polymer should be
>> near the center of box (please correct me if wrong)
> What you are seeing is a completely normal consequence of periodic
> boundary conditions.  You don't need to change the trajectory in any way to
> do density measurements; the resulting values will be the same before and
> after centering, since there is no "outside" or "center" of an infinite
> system.
> -Justin
>  So by doing this:
>> trjconv -f NPT_mdrun.trr -s NPT_mdrun.tpr -o NPT_mdrun_trjconv.trr -pbc
>> mol
>> -center
>> Select group for centering: I selected my polymer only
>> Select group for output: I selected all atoms (polymer + water + ions)
>> Please let me know is this correct way of modifying trajectory to
>> calculate
>> water and ion density?
>> regards,
>> Jiom
> --
> ==============================**==========
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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