[gmx-users] (no subject)

[Thomas Lipscomb]

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


Sincerely,
Thomas


On Saturday, November 8, 2014 7:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 





On 11/8/14 6:53 PM, Thomas Lipscomb wrote:
> Dear gmx-users,
>
> I am still following this tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
>
>
> But I got an error at this step:
> "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"):
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat"
>
>
> [tlipscomb at prime-radiant KALP]$ perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
> Eeeeek! No confout.gro at all!
>

As the error says, the file "confout.gro" does not exist.  Either (1) you named 
it something else, (2) energy minimization failed for some reason, or (3) it's 
somewhere else on your file system.

-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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