[gmx-users] problem with kalp simulation in DPPC

fatemeh razavineda21 at yahoo.com
Tue Jul 28 14:18:23 CEST 2015


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
and i want to know whether i should follow all of the steps or not
and when should i execute this command?
perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
 
after doing InflateGRO instructions?



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