g_sigeps(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_sigeps(1)NAME
g_sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_sigeps -o potje.xvg -[no]h -[no]version -nice int -[no]w -xvg enum -c6 real -cn real -pow int -sig real -eps real -A real -B real -C real
-qi real -qj real -sigfac real
DESCRIPTION
g_sigeps is a simple utility that converts C6/C12 or C6/Cn combinations to sigma and epsilon, or vice versa. It can also plot the poten-
tial in file. In addition, it makes an approximation of a Buckingham potential to a Lennard-Jones potential.
FILES -o potje.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-c6 real 0.001
c6
-cn real 1e-06
constant for repulsion
-pow int 12
power of the repulsion term
-sig real 0.3
sig
-eps real 1
eps
-A real 100000
Buckingham A
-B real 32
Buckingham B
-C real 0.001
Buckingham C
-qi real 0
qi
-qj real 0
qj
-sigfac real 0.7
Factor in front of sigma for starting the plot
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_sigeps(1)
Check Out this Related Man Page
g_anadock(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_anadock(1)NAME
g_anadock - cluster structures from Autodock runs
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_anadock -f eiwit.pdb -ox cluster.pdb -od edocked.xvg -of efree.xvg -g anadock.log -[no]h -[no]version -nice int -xvg enum -[no]free
-[no]rms -cutoff real
DESCRIPTION
g_anadock analyses the results of an Autodock run and clusters the structures together, based on distance or RMSD. The docked energy and
free energy estimates are analysed, and for each cluster the energy statistics are printed.
An alternative approach to this is to cluster the structures first using g_cluster and then sort the clusters on either lowest energy or
average energy.
FILES -f eiwit.pdb Input
Protein data bank file
-ox cluster.pdb Output
Protein data bank file
-od edocked.xvg Output
xvgr/xmgr file
-of efree.xvg Output
xvgr/xmgr file
-g anadock.log Output
Log file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[no]freeno
Use Free energy estimate from autodock for sorting the classes
-[no]rmsyes
Cluster on RMS or distance
-cutoff real 0.2
Maximum RMSD/distance for belonging to the same cluster
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_anadock(1)
Hey all, No sorry I don't mean burning windows. Though it was a nice thought to think of that people :) Pat yourself on the back for thinking of burning Windows.
No really though here the real question.
I'm after burning software for Solaris 7 (or 8 if it has to be, perfer 7 though). I... (1 Reply)
Hello AIX gurues...
In order to present the statistics of real memory usage I need to know how much real memory is used by the AIX 5L kernel. No the exact figures of course but some close to the reality.
The AIX is running in a 7GB real machine, it has a HACMP configuration and my concern is... (1 Reply)
I want to install grace (plotting package; formerly called "xmgr"; also called xmgrace) on a standard PC running Red Hat Linux. I was hoping to find someprecompiled executables, but I only found the complete source files with Makefiles, ".rpm" files, and ".so" files, but I am not experienced enough... (2 Replies)
I'm sure you guys have answered this elsewhere but I can't seem to find where so here goes.
#!/bin/bash
n=120
a=$(sed '120q;d' energy.xvg)
while ;do
a=$(sed $n'q;d' energy.xvg)
echo "$a \n" > newfile
n=$(($n+100))
done
exit 0
that script should read the file energy.xvg, start at... (1 Reply)
I am writing a text for LaTeX compile. I think that my grace figs need to be .ps or .eps files for incorporation. Can one just do a 'save as X.eps'
for this, or is another method required? Thanks- Marshall (6 Replies)
Hello there,
I'd like to define a variable b equal to 0.5/a where a=0.001, so I wrote something like that:
a=0.001;
let 'b=0.5/$a';
but it doesn't work... maybe because the variable a has a real value???
Any help will be appreciated!!!:D (1 Reply)
Dear all,
Im hoping you may be able to help with a little problem Im having using xmgrace.
I want to plot a dataset as a line curve e.g 1,2,3,4,5,6,15,16,17,18,19,20...
what i would like to do is not plot the missing bits of the sequence, i.e 1-6 would be a straight line then there would... (0 Replies)
Does anyone know for sure how to tell whether the RHEL 3 / 4 / 5 server you're logged into is real or VMware, other than rpm -qa | grep -i vm?
And if the server is real, is there any way to tell from the OS level what kind of hardware you're on? I guess I'm looking for something analogous to... (2 Replies)
Hi all.
So I have a problem. I have been doing real good figuring this stuff out on my own but Im a newbie and stuck on something that is probably real basic.
I want to get the following output from the who command:
User TTY Date Time
gd22a12 pts/1 Feb 1 11:34
gd22a13 pts/3 Feb 1... (13 Replies)
I'm curious if there is any real difference between using " " or ' ' or no quotes at all. For example, I have a variable called EXTRACT_FILES. When I declare it, I set it to false... EXTRACT_FILES=false. I eventually use the variable later in the script (having set it to EXTRACT_FILES=true due to... (2 Replies)
I have read enough books and know about all the basic commands in unix. I have practiced the same in my home. Now i want to real time work like scheduling cron in a real time server, creating alerts, application status check using unix etc..,
I want to have a real time server acc to do this kind... (3 Replies)