[gmx-users] (no subject)

Justin Lemkul jalemkul at vt.edu
Mon Nov 10 01:44:46 CET 2014

On 11/9/14 7:26 PM, Thomas Lipscomb wrote:
> Ok so to fix the adding ions error:
> number of coordinates in coordinate file (model1_solv.gro, 12266)
>               does not match topology (topol.top, 11116)

Like I said, you shouldn't be adding solvent or ions at this point.

>   I am redoing the shrinking steps:
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> 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
> Here is one iteration of the 26 shrinking steps:
> /usr/local/gromacs/bin/gmx grompp -f minim.mdp -c system_shrink1.gro -p topol.top -o em.tpr
> /usr/local/gromacs/bin/gmx mdrun -s em.tpr -v
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Is that correct?  Do I just copy and paste it into the command line 26 times to iterate it 26 times?

No.  First, you're still repeating file names, and second, simply doing the same 
thing 26 times will give you nothing of any use.  You need to progressively 
shrink the lipids around the protein.

Shrink -> obtain system_shrink1.gro
Minimize -> obtain em1.gro (or whatever)
Shrink -> input is em1.gro and output is system_shrink2.gro
Minimize -> obtain em2.gro

Note that the file names (1, 2,...) indicate how many shrinking steps you've 
done.  You loop over the commands, using the output of the previous step as the 
input into the next.



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


More information about the gromacs.org_gmx-users mailing list