On 2012-11-15 18:53, shch406 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?
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).
Thanks in advance,
Igor Shchechkin
I think you need to switch the arguments, first side chain then water.
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell Molec. Biol., Uppsala University.
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