Hi,
I calculated the radial distribution functions with ptraj for a ligand in a
box of water. However, no matter which two atoms I pick, the rdf output turn
out the same. Even if I randomly select any water molecules as centers, the
rdf is still the same.
Here is the script I do rdf with:
trajin ../mdcrd 1 100 1
center .405
radial rdf_1 0.2 5.0 :HOH.O
center .1009
radial rdf_2 0.2 5.0 :HOH.O
The ptraj output does not seem wrong to me:
PTRAJ: center .405
Mask [.405] represents 1 atoms
PTRAJ: radial rdf_1 0.2 5.0 :HOH.O
Mask [:HOH.O] represents 426 atoms
PTRAJ: center .1009
Mask [.1009] represents 1 atoms
PTRAJ: radial rdf_2 0.2 5.0 :HOH.O
Mask [:HOH.O] represents 426 atoms
[No output trajectory specified (trajout)]
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 100 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (../mdcrd) is an AMBER trajectory (with box info) with 100 sets
NO OUTPUT COORDINATE FILE WAS SPECIFIED
ACTIONS
1> CENTER to box center via center of geometry, atom selection follows
:135.H
2> RADIAL DISTRIBUTION FUNCTION: Output to rdf_1
spacing is 0.200
maximum is 5.000
[This implies 25 bins]
density is 0.033
RDF will represent all atoms in the solvent mask
Solvent atom selection is :2-427.O
3> CENTER to box center via center of geometry, atom selection follows
:337.O
4> RADIAL DISTRIBUTION FUNCTION: Output to rdf_2
spacing is 0.200
maximum is 5.000
[This implies 25 bins]
density is 0.033
RDF will represent all atoms in the solvent mask
Solvent atom selection is :2-427.O
So why do I get identical rdfs for different atoms? Thanks in advance.
Dian
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Received on Mon Feb 15 2010 - 13:00:02 PST
