[AMBER] RDF with ptraj

From: Dian Jiao <oscarjiao.gmail.com>
Date: Mon, 15 Feb 2010 13:45:00 -0700

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
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