[gmx-users] (no subject)

Thomas Lipscomb linuxborg2 at yahoo.com
Sun Nov 9 18:40:39 CET 2014

So I do this?:

perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink2.gro 5 area_shrink2.dat
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink3.gro 5 area_shrink3.dat
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink26.gro 5 area_shrink26.dat

On Saturday, November 8, 2014 9:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 11/8/14 8:52 PM, Thomas Lipscomb wrote:
> Ok I am further along, now at:
> "Follow this up by another round of EM. During the "shrinking" steps, be sure to
> change the cutoff value to 0, or else you will continue to delete lipids! After
> 26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 Å2,
> above the experimental value of ~62 Å2. Since the script tends to overestimate
> the area per lipid, this value is good enough to continue to equilibration."
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
> My best guess on how to do that is this:
> /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c confout.gro -p topol_dppc.top
> -o em2.tpr
> /usr/local/gromacs/bin/gmx mdrun -s em2.tpr -v (THIS IS THE SECOND ENERGY
> plus some perl commands
> Because I'm repeating what I did before:
> /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top
> -o em.tpr
> /usr/local/gromacs/bin/gmx mdrun -s em.tpr -v
> I'm having trouble figuring out how to do 26 iterations

You don't need topol_dppc.top for anything except making DPPC whole.  Ignore 
those files after you've accomplished this.

It boils down to understanding what InflateGRO is suppose to do.  Once you start 
compressing/shrinking the lipids, you minimize after each step and compress some 
more.  So you minimize the output of shrink step 1, which is then input into 
InflateGRO to shrink again (shrink2), minimized, input into InflateGRO...



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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