[gmx-developers] remove periodicity

[Anton Feenstra]

On 02/07/10 23:24, Gaurav Goel wrote:
> 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.
>>
>
> Thanks for your reply Anton. I need to modify the md
> 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.

Just a not of caution, if you are going to modify the md code, do *not* 
use code from trjconv. The latter is meant for analysis, and uses some 
constructions that should not be used during simulation (md or otherwise).

> 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.

This is not my main expertise, but AFAIK the non-bonded interaction code 
and the related neigbour-search code optimizes best with all atoms in 
the box.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam     |
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