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GROMACS Tutorial
ns_type
morse
coulombtype
vdw_type
rlist
rcoulomb
rvdw
rcoulomb_switch
rvdw_switch
epsilon_r
Tcoupl
Pcoupl
gen_vel
=
=
=
=
=
=
=
=
=
=
=
=
=
grid
no
Shift
Shift
1.4
1.2
1.2
1.0
1.0
6.0
no
no
no
; Conjugate gradient with morse potential
;
in vacuo
;
User kerrigan (236)
;
;
Input file
;
cpp
= /usr/bin/cpp
constraints
= none
integrator
= cg
nsteps
= 3000
;
;
Energy minimizing stuff
;
emtol
= 100
emstep
= 0.01
nstcgsteep
= 1000
nstcomm
morse
coulombtype
vdw_type
ns_type
rlist
rcoulomb
rvdw
rcoulomb_switch
rvdw_switch
epsilon_r
Tcoupl
Pcoupl
gen_vel
=
=
=
=
=
=
=
=
=
=
=
=
=
=
1
yes
Shift
Shift
grid
1.4
1.2
1.2
1.0
1.0
6.0
no
no
no
The g_rmsf command may also be used to compute temperature factors. The computed
temperature factors can be compared to x-ray crystal structure temperature factors.
g_rmsf –s md.tpr –f md.xtc –o rmsf.xvg –oq fws_bfac.pdb
Use the “Backbone” group once again.
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