[gmx-users] editconf & genbox for Constraint Pull
vuh105 at psu.edu
Mon Jul 14 16:44:47 CEST 2008
I am pulling a 17 amino acid peptide under constraint pulling. Some details:
v = 0.01 nm/ps
dt = 0.002 ps
steps = 250000
total time = 500 ps
My question is: When generating the water box for the simulation, I understand
that the edge of the box should be greater than half the cutoff distance. But
because the peptide will be stretched a distance of 5 nm by the end of the
simulation, is it necessary that the peptide be placed in a box that is > 5nm
from the edge of the box? If my cutoff distance is 1.5 nm, will 0.8 nm be
sufficient. i.e., which of the below code would be appropriate. I AM using
periodic boundary conditions.
editconf -f E_min_protein.gro -o E_min_protein_box.gro -bt cubic -d 5.50
editconf -f E_min_protein.gro -o E_min_protein_box.gro -bt cubic -d 0.80
I have tried both scenarios. The only problem I have is that if the protein is
placed in a water box whose edge is placed 5.5 nm from the protein, the
simulation takes almost 3 days and 60 Gb. Any tips on reducing the information
in the output file? Any help is appreciated.
Pennsylvania State University
Schreyer Honors College
Undergraduate - Bioengineering
"You must be the change you wish to see in the world."
--Mohandas Karamchand Gandhi
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