AMBER: RDF of pure chloroform

From: BJÍRN KARLSSON <BJORN.KARLSSON.hik.se>
Date: Mon, 25 Jun 2007 17:56:19 +0200

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/┼^3) using the radial command in PTRAJ.

Here is my input:

trajin eq200ps.mdcrd
radial rdf_cl3 0.01 20 :CL3.C1 :CL3.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/┼^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/Bj÷rn


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Received on Wed Jun 27 2007 - 06:07:21 PDT
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