On 10/2/12 2:16 PM, James Starlight wrote:
Dear all!
Recently I've forced with the same problem as was in this topic :)
I have tieleman's lipids consisted of 128 dppc with water.
also I have system with the protein inserted in the same bilayer
I wounder to know
1- How I could change lipid number in the pure lipid bilayer (
increase up to 200 lipids) with standard Gromacs tools ?
I've tried use
genbox -cs dppc128_whole.gro -box 8.04542 8.04542 10.19156
where 8.045 in x and y was higher than in the case of initial bilayer ( 6.045)
As the consequence that prodyce larger system with increased amount of
water in upper and lower layers but the lipid number was the same.
The proper approach is to set values for the box that are larger in x and y, but
the same size in z. That way, the new "solvation" occurs within the same plane
as the membrane.
2- Is there any way to increase lipid number ( to add lipids from each
size of the system) in the bilayer with the inserted protein ?
Using the same approach, with a slight modification:
genbox -cp protein_in_membrane.gro -cs dppc128_whole.gro -box (x y z)
Increase the values of x and y, and leave z alone.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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