On 11/15/12 2:28 PM, Dr. Vitaly Chaban wrote:
Dear Gromacs users,
I tried g_rdf function and have obtained a strange result:
usually the RDF curve looks like relaxing oscillations around 1.0 constant
level,
but in my case it appears to be oscillation around exponent going from 0.0
at zero distance to 1.0 at large distances.
Is the RDF obtained correct?
No. It is not correct.
I used the command as follows:
g_rdf -f MT.trr -s MT.tpr -n rs.ndx -o MT.RD.xvg -bin 0.05 -pbc -rdf res_cog
where file MT.trr contains ~150 ps of equilibrated trajectory of 582 residue
protein in water;
The "reference group" was chosen "Water" and the "1 group" was taken from
index file rs.ndx.
The latter group contains two tip NHH groups of charged arginine. (This
residue was inspected
on exposing to solvent and showed one of the largest solvent accessible
surface).
I would have chosen the groups in the opposite manner. You're interested in the
presence of water around the chosen arginine residue, not the presence of
arginine around water, right? Given this order of chosen groups, the RDF seems
to make sense (very low probability that arginine is close to all water
molecules), though it doesn't represent what you likely want.
-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
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