On 19/01/2012 11:27 PM, Chandan Choudhury wrote:
On Thu, Jan 19, 2012 at 3:49 PM, Tsjerk Wassenaar <tsje...@gmail.com
<mailto:tsje...@gmail.com>> wrote:
Hi Chandan,
The box is accessible from the t_trxframe struct. Assuming you have
t_trxframe *fr
You can access it through
fr->box
Thanks Tsjerk. It (fr.box) did help me to get the box coordinates.
fr.box[XX][XX], fr.box[YY][YY] and fr.box[ZZ][ZZ] gives me the values
but fr.box[XX][YY], fr.box[XX][ZZ] prints 0. Which seems to me that
the origin of the box is at (0,0,0).
The origin is always at (0,0,0) by definition, not by the contents of
fr.box. There's no magic center of a periodic box, either.
fr.box has the box dimensions, which in general require more than the 3
pieces of information required for a rectangular solid box.
Then, fr.box[XX][XX] is the maximum X-coordinate, fr.box[YY][YY] is
the maximum Y-coordinate,fr.box[ZZ][ZZ] is the maximum Z-coordinate.
Am I correct?
For some box types, yes.
Mark
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.
Yeah, you are right.
Chandan
Hope it helps,
Tsjerk
On Thu, Jan 19, 2012 at 11:14 AM, Chandan Choudhury
<iitd...@gmail.com <mailto:iitd...@gmail.com>> wrote:
>
>
> On Thu, Jan 19, 2012 at 12:17 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@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
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