[gmx-users] getting rid of PBC, completely

[Chandan Choudhury]

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<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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