[gmx-users] problem with kalp simulation in DPPC

[Justin Lemkul]

On 7/28/15 8:18 AM, fatemeh wrote:
> Hello
>
> 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.

-Justin

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

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