[gmx-users] getting rid of PBC, completely

[Tsjerk Wassenaar]

Hi Chandan,

The box is accessible from the t_trxframe struct. Assuming you have

t_trxframe *fr

You can access it through

fr->box

But if you remove jumps first, you're fine anyway. Just don't put
things back in the box afterwards. And don't center if your aim is
calculating MSDs.

Hope it helps,

Tsjerk

On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury <iitdckc at gmail.com> wrote:
>
>
> On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
>>
>> On 19/01/2012 5:39 PM, Chandan Choudhury wrote:
>>>
>>>
>>> Dear gmx-users,
>>>
>>> I have a simulated a system containing a linear polymer in a cubic box
>>> with water molecules.  I need to get rid of PBC effect on the system such
>>> that I can execute my own analysis code. I intend to compute the msd of
>>> water molecules along the polymer backbone.
>>
>>
>> You can't "get rid of PBC", you can only manage it. The question reduces
>> what you want to see if a molecule diffuses across the periodic boundary
>> from near one end of the polymer to the other end.
>>
>>
>>> So, when I execute my own analysis code, I see the msd's are abrupt (i.e
>>> very high), this is due to the pbc. So, for getting rid of PBC effect, I
>>> performed the suggested trjconv workflow
>>> (http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions).
>>>
>>> Below are my executed commands :
>>>
>>> # Made the system whole
>>>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o
>>> 0-4_whole.xtc
>>>
>>> # 0 is the whole system. md0-4.tpr is the initial tpr file containing
>>> whole (no broken) polymer inside the cubic box.
>>> # Extracted 1st frame from the initial trajectory
>>>
>>> echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump  -o 1st.pdb
>>> -dump 0
>>>
>>> # used the whole trajectory to remove jumps with reference to the 1st
>>> frame.
>>> echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o
>>> 0-4_nojump.xtc
>>
>>
>> So here you said "let molecules diffuse away from the solute".
>>
>>
>>>
>>> #system is being centered
>>> echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o
>>> 0-4_center.xtc -center
>>>
>>> #putting every atom in the box
>>> echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom
>>
>>
>> ... and now you said "take all the atoms and put them back in the box",
>> creating jumps whenever one crosses the boundaries.
>>
>>
>>>
>>> Still when I execute my analysis code, I do see the abrupt behaviour in
>>> the msd plot. Can someone guide me how to completely get rid of PBC
>>> artifacts.
>>
>>
>> Don't simulate with them :-P Is your analysis technique sound for the
>> periodic case?
>
>
> No, my analysis code doesnot take care of PBC. As to deal with PBC, I need
> to have the box vectors (for atleast NPT simulation) from the trajectory and
> I am unable to extract the box vectors (as of date).
>
> Chandan
>
>>
>>
>> Mark
>>
>> --
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>
>
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands