[gmx-users] Re: Strange form of RDF curve

Justin Lemkul jalemkul at vt.edu
Thu Nov 15 22:15:05 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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