On 7/4/12 1:31 PM, Dr. Vitaly V. G. Chaban wrote:
Dear GROMACS people -
I am calculating radial distribution function between the centers of
mass of two large particles in a periodic box.
My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f
conf.gro
My index file contains two groups of atoms standing for the first and
the second supraparticles whose centers-of-mass I am interested in.
Since here I provide the "conf.gro" file rather than a trajectory, I
expect to get just one peak in my RDF, but instead I get multiple
peaks at different separation distances (please, see
http://i47.tinypic.com/24m826v.jpg). The groups of atoms in the index
file are separated spatially, if this may matter.
Would anyone kindly explain how the COM RDF function works? My
ultimate purpose is to depict how the distance between those two
centers-of-mass evolves in time.
You also need to use the -com flag to use the COM of the reference group.
-Justin
The -com flag changed the output (please, see
http://i48.tinypic.com/29uuo7b.jpg) but there is still a number of
embarassing peaks after 7nm. Given the positions of these
supraparticles, I would expect maximum about 10nm whereas the box side
is 26nm.
From the g_rdf help message --
The option -rdf sets the type of RDF to be computed. Default is for atoms or
particles, but one can also select center of mass or geometry of molecules or
residues. In all cases, only the atoms in the index groups are taken into
account.
I understand this in the following way. The centers-of-mass of the
groups in the index file are computed and further the calculation
proceeds as if these COMs were regular atoms. If I have only two
groups, I should get one maximum.
Am I not correct?
In theory, yes. I have no idea how effective g_rdf is for this purpose. From
your initial description, if you're just trying to track COM distance over time,
why not use g_dist? That's precisely what it does.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
