Anirban Ghosh wrote:
Hi ALL,
I have a system of a GPCR protein in a lipid bilayer. I want to extend
the water layer along the negative Z-direction. I found a script by Chris
at the GROMACS mail list. But I am unable to use it properly. Can anyone
please explain how to use it to extend the water layer only in the
negative Z-direction. And also what does "upeerz and lowerz" signify? Is
it for the protein or the water layers? Thanks a lot in advance.
If the script isn't working out for you, there is another approach. Position
your system within the appropriately-sized box with editconf (specifying the
appropriate -center), then use genbox, i.e.:
http://wiki.gromacs.org/index.php/Membrane_Simulations#Adding_waters_with_genbox
If you have placed the membrane appropriately, genbox will fill the rest of the
empty space with water.
-Justin
Regards,
*Anirban Ghosh*
*Grade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
*
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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