[gmx-users] (no subject)
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."
> 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
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users