[gmx-users] (no subject)

[Thomas Lipscomb]

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 MINIMIZATION)

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

Sincerely,
Thomas


On Saturday, November 8, 2014 7:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 




On 11/8/14 7:35 PM, Thomas Lipscomb wrote:
> Ok so the tutorial did not give me the energy minimization command I have to find it and execute it before I can do perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
>
> The manual has 3 different types to choose from:
> 3.10 Energy Minimization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
> 3.10.1 Steepest Descent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
> 3.10.2 Conjugate Gradient . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
> 3.10.3 L-BFGS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
>
> I'm sorry but I don't know what to do.  The good news is that I already have minim.mdp
>

The membrane tutorial is considered somewhat advanced, as I don't spell out 
exactly what to do.  As the introduction states, it assumes you are familiar 
with what "run energy minimization" would mean.  If you have a suitable .mdp 
file, you have coordinates, and you have a topology...that's all you need to run 
grompp.


-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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