[gmx-users] problem with kalp simulation in DPPC
jalemkul at vt.edu
Tue Jul 28 15:54:06 CEST 2015
On 7/28/15 8:18 AM, fatemeh wrote:
> I am a new user of gromacs. i have two problems while practicing
> simulation of Kalp15 in DPPC Dr Justine Lemkul tutorial
> i have problem with this part
> "genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> In the .mdp file used for the minimizations, add a line "define = -
> DSTRONG_POSRES" to make use of these new position restraints. Then, simply
> follow the InflateGRO instructions (contained in the script itself), a
> procedure that is easily scripted. Scale the lipid positions by a factor
> of 4:
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat"
> first i cannot find InflateGRO instructions
That's what the above command is.
> and i want to know whether i should follow all of the steps or not
Tutorial steps are not optional. Follow them exactly.
> and when should i execute this command?
When the tutorial tells you to.
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> after doing InflateGRO instructions?
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
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