[gmx-users] Re: Extend water layer along negative Z-direction

2009-07-16 Thread Kirill Bessonov 
You can try to position your system in Z direction using:

editconf -princ  (and bunch of other normal parameters)

Also you can use -rotate parameter to align your system along any axis

Hope it helps
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[gmx-users] Re: Extend water layer along negative Z-direction

2009-06-01 Thread Anirban Ghosh 

Hi ALL,

Thanks a lot Chris, Justin and Tsjerk for yor replies.
Actually, my problem is not fully resolved. A portion of the protein tail is 
outside the water box in the Z direction (coordinate in Z is -35). So as 
suggested by you when I am issuing the command editconf -f box.gro -o BOX.gro 
-box 0 0 -3.5, but after that genbox is giving the error:

Fatal error:
Undefined solute box.
Create one with editconf or give explicit -box command line option

Please can you specify the proper command, so that the water box is extended 
only in the negative Z direction (to solvate the portion of the protein out of 
the box)

Regards,



 Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India



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Re: [gmx-users] Re: Extend water layer along negative Z-direction

2009-06-01 Thread Tsjerk Wassenaar 
Hi Anirban,

You have to get a grip on PBC. What you're suggesting is like
extending the earth only westward, but not eastward as something is
sticking out in only one direction. It's impossible! The system is
periodic.The box vectors are direction vectors, indicating the
periodicity. Moreover, you're command to extend the box (-box 0 0
-3.5) tries to set a box with vector _lengths_ 0, 0 and -3.5. Maybe a
good idea to read Chapter 3 of the manual, regarding periodic boundary
conditions.

Cheers,

Tsjerk

On Mon, Jun 1, 2009 at 8:24 AM, Anirban Ghosh anirban...@yahoo.co.in wrote:

 Hi ALL,

 Thanks a lot Chris, Justin and Tsjerk for yor replies.
 Actually, my problem is not fully resolved. A portion of the protein tail is
 outside the water box in the Z direction (coordinate in Z is -35). So as
 suggested by you when I am issuing the command editconf -f box.gro -o
 BOX.gro -box 0 0 -3.5, but after that genbox is giving the error:

 Fatal error:
 Undefined solute box.
 Create one with editconf or give explicit -box command line option

 Please can you specify the proper command, so that the water box is extended
 only in the negative Z direction (to solvate the portion of the protein out
 of the box)

 Regards,




 Anirban Ghosh
 Grade Based Engineer
 Bioinformatics Team
 Centre for Development of Advanced Computing (C-DAC)
 Pune, India

 
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
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