# [gmx-developers] remove periodicity

Gaurav Goel gauravgoeluta at gmail.com
Fri Jul 2 23:24:42 CEST 2010

```On Fri, Jul 2, 2010 at 3:20 AM, Anton Feenstra <feenstra at few.vu.nl> wrote:
> On 01/07/10 22:22, Gaurav Goel wrote:
>>
>> If I know the coordinates at time 't-del_t' and 't', I can remove the
>> periodicity as follows:
>>   /* Remove periodicity */
>> ...
>> ...
>>
>>       while(xcur[ind][m]-xprev[ind][m]<= -hbox[m])
>>        rvec_inc(xcur[ind],box[m]);
>>       while(xcur[ind][m]-xprev[ind][m]>   hbox[m])
>>        rvec_dec(xcur[ind],box[m]);
>> ...
>> ...
>
> What do you mean with 'remove periodicity'? Make molecules whole? Put all
> atoms in the box? Put all molecules' center of mass in the box? Give all
> atoms (or molecules) a continuous trajectory (i.e., they will fly 'out of
> the box')?
>
> There are a number of PBC related options in trjconv that might include what
> you want. If you want to use that in a program of you own, I suggest copying
> over the routine(s) from trjconv.
>

algorithm...basically scale the velocities of atoms up or down in two
slabs at a fixed distance from the face of the box. By "remove
periodicity" I meant to put all atoms in the box.

>> ->  If I only know the coordinates at 't', is it still possible to
>> remove periodicity?
>> In the update() subroutine, I want to be able to make a list of all
>> atoms within a thin slab at a fixed distance from the edge of the box.
>> E.g., all particles in a slab of width L/10, with the x-coordinate of
>> the center of slab at a distance L/4 from the yz-face of box.
>
> During md integration (i.e., in update() within mdrun), molecules are made
> whole to calculate bonded interactions, and atoms are put in the box for the
> non-bonded interactions. If you put your code in the proper place, you
> should catch the coordinates in the 'atoms in the box' state, and you don't
> have to worry about the PBC. You'll have to invest some time to get to
> understand the code, since it is quite involved.
>

I will take a further look at the md algorithm and try to locate where
in the code coordinates are generated corresponding to 'atoms in the
box' state. I am not able to understand why atoms need to be put in
the box to calculate non-bonded interactions? Isn't it right that for
non-bonded interactions we need the closest periodic image.

-Gaurav
>
> --
> Groetjes,
>
> Anton
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
> |(   |   )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands  |
> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 |
> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
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```