g_saltbr(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_saltbr(1)NAME
g_saltbr - computes salt bridges
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_saltbr -f traj.xtc -s topol.tpr -[no]h -[no]version -nice int -b time -e time -dt time -t real -[no]sep
DESCRIPTION
g_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.
FILES -f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-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
trunc distance
-[no]sepno
Use separate files for each interaction (may be MANY)
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_saltbr(1)
Check Out this Related Man Page
g_dist(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_dist(1)NAME
g_dist - calculates the distances between the centers of mass of two groups
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -lt lifetime.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum
-dist real
DESCRIPTION
g_dist can calculate the distance between the centers of mass of two groups of atoms as a function of time. The total distance and its
x-, y-, and z-components are plotted.
Or when -dist is set, print all the atoms in group 2 that are closer than a certain distance to the center of mass of group 1.
With options -lt and -dist the number of contacts of all atoms in group 2 that are closer than a certain distance to the center of mass
of group 1 are plotted as a function of the time that the contact was continuously present.
Other programs that calculate distances are g_mindist and g_bond.
FILES -f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-n index.ndx Input, Opt.
Index file
-o dist.xvg Output, Opt.
xvgr/xmgr file
-lt lifetime.xvg Output, Opt.
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-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)
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-dist real 0
Print all atoms in group 2 closer than dist to the center of mass of group 1
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_dist(1)
how can i read input to quit any time, for instance "type q to quit"
I have a script like this
echo "The first choice"
read firstChoice
echo "The second choice"
read secondChoice
Looking for a code to quit any time by pressing q to quit
any help would be appreciated
thanks (5 Replies)
i have a script that will do the following:
1) find the 5 min before time from the current time
2) Grep the data from a file from current time to the 5 min before time
below the code:
#!/bin/ksh
current_time=`date +%s`
echo "$current_time"
perl -le 'print scalar... (3 Replies)
Can someone please help me with searching a string during a specific time frame. Below is the format of the time from my log file.
"GET /AAM2009_wherewereheaded.wmv HTTP/1.1" 200 52307085
The search string I need is "AAM2009_wherewereheaded.wmv"
I need to search the number of... (1 Reply)
I am trying to list the name of files on an MOD - I use the command
tar vtf /MOD_DRIVE|more
and I get a nice list of filenames/directories on this particular MOD. When I put in another MOD that contains software options I get the error "directory checksum error". I would like to be able to... (2 Replies)