VENKATESH HARIHARAN wrote:
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
or
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.
I can't comment on the setup, but in terms of the output, you can change the
amount of output data you get in the .mdp file, reducing the frequency of saving
coordinates, velocities, etc. (nstxout, nstvout, and others). I'm guessing the
.trr file is what's getting out of hand, so modifying those two options should
help some.
-Justin
______________________________
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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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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