GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  GMX-SALTBR (1)

NAME

gmx-saltbr - Compute salt bridges

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>]
[-t <real>] [-[no]sep]

DESCRIPTION

gmx saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways. A minimum distance can be given (i.e. a cut-off), such that groups that are never closer than that distance will not be plotted.

Output will be in a number of fixed filenames, min-min.xvg, plus-min.xvg and plus-plus.xvg, or files for every individual ion pair if the -sep option is selected. In this case, files are named as sb-(Resname)(Resnr)-(Atomnr). There may be many such files.

OPTIONS

Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa

Other options:

-nice <int> (19)
Set the nicelevel

-b <time> (0)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-dt <time> (0)
Only use frame when t MOD dt = first time (ps)

-t <real> (1000)
Groups that are never closer than this distance are not plotted

-[no]sep (no)
Use separate files for each interaction (may be MANY)

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

Search for    or go to Top of page |  Section 1 |  Main Index


VERSION 5.0.6 GMX-SALTBR (1)

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.