[gmx-users] confout.gro

Justin Lemkul jalemkul at vt.edu
Tue Jul 8 13:46:33 CEST 2014

On 7/8/14, 6:16 AM, RINU KHATTRI wrote:
> hello every one
> now i am using command
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr -maxwarn
> mdrun -deffnm em
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat
>   so i have to follow all four command again and again or any thing
> else i am using second third and fourth command but all time result is
> same

You don't repeat commands verbatim over and over again.  Think about it - that 
wouldn't accomplish anything; you'd just keep doing the same manipulations on 
the same coordinates.  Do you understand the approach that is being applied here?

The above sequence is not even correct; you appear to be trying to do an energy 
minimization of just DPPC.  Follow the tutorial exactly and don't issue commands 
out of order.  Visualize the output of every step so you understand what is 
going on.  There is a reason this approach and the tutorial itself are a bit 
more advanced; I can't spell out every single detail here.

To (very) briefly summarize what you need to do: if you have successfully 
inflated, minimized, and shrunk the system once, you need to take the current 
output (system_shrink1.gro) and minimize it.  I would suggest avoiding default 
file names here to avoid confusion.  Call the minimized structure confout1.gro 
instead of just confout.gro, and then shrink that again by a fact of 0.95 to 
create system_shrink2.gro, then minimize that (obtain confout2.gro), shrink 
it...on and on until you achieve a sensible structure, as judged by the APL.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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