[gmx-users] editconf & genbox for Constraint Pull

VENKATESH HARIHARAN vuh105 at psu.edu
Mon Jul 14 16:44:47 CEST 2008

Hello all,

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.


Venkatesh Hariharan
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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