[gmx-users] editconf & genbox for Constraint Pull

Justin A. Lemkul jalemkul at vt.edu
Mon Jul 14 18:12:08 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
> 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.


> ______________________________
> 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


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