[gmx-users] Is it correct

[shahrbanoo karbalaee]

Dear justin
In my work MD peptide(with 13 aa) I use this md.mdp.would ypu please
say me Is that correct.

title               =  cpeptide MD
cpp                 =  /lib/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  5000     ; total 5 ps.
nstcomm             =  1
nstxout             =  50
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tau_t               =  0.1      0.1
tc-grps             =  protein  sol
ref_t               =  300      300
; Pressure coupling is not on
Pcoupl              =  no
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

-- 
2)In the place program doesent have phrase for example PME,....does.
the gromacs use default?
3)when I use berendsen coupling is on and pcoup =yes and In my work is
 effect in fluctuate?

best
sh-karbalaee