AMBER Archive (2007)

Subject: AMBER: RDF of pure chloroform

From: BJÖRN KARLSSON (BJORN.KARLSSON_at_hik.se)
Date: Mon Jun 25 2007 - 10:56:19 CDT

Hi Amer Users!

I am currently doing MD simulations at NVT of a pure solutions of chloroform (100 molecules)
from my trajectory of 200ps I am interested to construct a RDF using the user input density of chloroform instead of water (0.0334 molecule/Å^3) using the radial command in PTRAJ.

Here is my input:

trajin eq200ps.mdcrd
radial rdf_cl3 0.01 20 :CL3_at_C1 :CL3_at_C1 density 0.00776

Here I have chosen to use the same atom on chloroform as both solute and solvent atoms and calculated the chloroform density as described in the amber-manual as (6.022/(10*119.38))*density of chloroform to 0.00776 molecules/Å^3 (119.38 g/mol is the molecular weight of chloroform).

However when I get my output-files rdf_cl3_standard.xmgr which I know is the only file being affected by my input density, The RDF does not approximate 1 for longer atom distances.

What am I doing wrong?

Any resonse is welcome/Björn

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