g_pme_error(1) GROMACS suite, VERSION 4.5.4-dev-20110410-e5eb052-dirty g_pme_error(1)NAME
g_pme_error - estimates the error of using PME with a given input file
VERSION 4.5.4-dev-20110410-e5eb052-dirty
SYNOPSIS
g_pme_error -s topol.tpr -o error.out -so tuned.tpr -[no]h -[no]version -nice int -beta real -[no]tune -self real -seed int -[no]v
DESCRIPTION
g_pme_error estimates the error of the electrostatic forces if using the sPME algorithm. The flag -tune will determine the splitting
parameter such that the error is equally distributed over the real and reciprocal space part. The part of the error that stems from self
interaction of the particles is computationally demanding. However, a good a approximation is to just use a fraction of the particles for
this term which can be indicated by the flag -self.
FILES -s topol.tpr Input
Run input file: tpr tpb tpa
-o error.out Output
Generic output file
-so tuned.tpr Output, Opt.
Run input file: tpr tpb tpa
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-beta real -1
If positive, overwrite ewald_beta from .tpr file with this value
-[no]tuneno
Tune the splitting parameter such that the error is equally distributed between real and reciprocal space
-self real 1
If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles
-seed int 0
Random number seed used for Monte Carlo algorithm when -self is set to a value between 0.0 and 1.0
-[no]vno
Be loud and noisy
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Sun 10 Apr 2011 g_pme_error(1)
Check Out this Related Man Page
g_rama(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rama(1)NAME
g_rama - computes Ramachandran plots
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_rama -f traj.xtc -s topol.tpr -o rama.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum
DESCRIPTION
g_rama selects the phi/psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix
tools such as grep you can select out specific residues.
FILES -f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Run input file: tpr tpb tpa
-o rama.xvg Output
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)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_rama(1)
Hi,
I have a .txt file which contains the x, y and z co-ordinates of particles which I am trying to cast for a particular compound. The no. of particles present is of the order of 2 billion and hence the size of the text file is of the order of a few Gigabytes. The particles have been casted layer... (5 Replies)
hi,
In my script, i wrote a line like this : ls -lrt tpa* > x.xls
while executing the script, it showing o/p as "tpa*: No such file or directory" because there is no files starts with tpa*
now, instead of server showing this msg, i want my scritpt to display as : "No jobs available which... (15 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)