1GMX-RAMA(1)                         GROMACS                        GMX-RAMA(1)
2
3
4

NAME

6       gmx-rama - Compute Ramachandran plots
7

SYNOPSIS

9          gmx rama [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-o [<.xvg>]] [-b <time>]
10                   [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
11

DESCRIPTION

13       gmx  rama  selects the phi/psi dihedral combinations from your topology
14       file and computes these as a function of time.  Using simple Unix tools
15       such as grep you can select out specific residues.
16

OPTIONS

18       Options to specify input files:
19
20       -f [<.xtc/.trr/…>] (traj.xtc)
21              Trajectory: xtc trr cpt gro g96 pdb tng
22
23       -s [<.tpr>] (topol.tpr)
24              Portable xdr run input file
25
26       Options to specify output files:
27
28       -o [<.xvg>] (rama.xvg)
29              xvgr/xmgr file
30
31       Other options:
32
33       -b <time> (0)
34              Time of first frame to read from trajectory (default unit ps)
35
36       -e <time> (0)
37              Time of last frame to read from trajectory (default unit ps)
38
39       -dt <time> (0)
40              Only use frame when t MOD dt = first time (default unit ps)
41
42       -[no]w (no)
43              View output .xvg, .xpm, .eps and .pdb files
44
45       -xvg <enum> (xmgrace)
46              xvg plot formatting: xmgrace, xmgr, none
47

SEE ALSO

49       gmx(1)
50
51       More     information    about    GROMACS    is    available    at    <‐
52       http://www.gromacs.org/>.
53
55       2019, GROMACS development team
56
57
58
59
602019.4                           Oct 02, 2019                      GMX-RAMA(1)
Impressum