James Starlight wrote:
Justin,
So It seems that I've done all steps in accordance to that workflow and
there have not been any more errors during loading my system in the
gromp. :)
By the way I have some methodological questions
1- Could you provide me with the source of the initial single lipids?
Previously I've done my system based on the VMD plugin for bilayer
constructing but I want to find single lipids and prepared my system
by-hands.
Here are several:
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources
2- Could you tell me other possible methods for self bi-layer
preparation starting from initial single lipid molecule ?
Packmol is a program that can build bilayers. You can also build crude
monolayers with Gromacs that can be manipulated with genconf -nbox. These would
require significant equilibration, as they are artificially crystalline.
-Justin
Thanks again,
James
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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