AMBER Archive (2008)

Subject: AMBER: Radial Distribution Function

From: prabhakar g (prabha.kaist_at_gmail.com)
Date: Mon Dec 08 2008 - 20:37:52 CST

Dear Amber experts,

I have carried out a 1ns restrained md simulation of I2(iodide) molecule in
MEOHBOX using ff99 force field,
(force constant of 100 kcal/mol)
Here is my simulation protocol using sander(Amber9)(from tutorial)
Minimization I (restrained minimization)
Minimization II ( whole system minimization)
Heating 20ps(NVT)
equilibration 300ps (NPT)
production 1ns (NVT)

am interested in calculating the radial distribution function(rdf) for
studies related to photo-dissociation.
I calculated the rdf with ptraj but for some of the atomic pairs i am
getting an unusual rdf
that is the curve does not converges to 1 for some of the atomic pairs (
file attached)
here is my ptraj input

trajin i2_meoh_md1.2ns.mdcrd
radial rdfC1-I1.out 0.1 15.0 :2-569_at_C1 :1_at_I1 density 0.015036
radial rdfC1-I2.out 0.1 15.0 :2-569_at_C1 :1_at_I2 density 0.015036
radial rdfO1-I1.out 0.1 15.0 :2-569_at_O1 :1_at_I1 density 0.015036
radial rdfO1-I2.out 0.1 15.0 :2-569_at_O1 :1_at_I2 density 0.015036
radial rdf1HC-I1.out 0.1 15.0 :2-569_at_1HC :1_at_I1 density 0.015036
radial rdf1HC-I2.out 0.1 15.0 :2-569_at_1HC :1_at_I2 density 0.015036
radial rdf2HC-I1.out 0.1 15.0 :2-569_at_2HC :1_at_I1 density 0.015036
radial rdf2HC-I2.out 0.1 15.0 :2-569_at_2HC :1_at_I2 density 0.015036
radial rdf3HC-I1.out 0.1 15.0 :2-569_at_3HC :1_at_I1 density 0.015036
radial rdf3HC-I2.out 0.1 15.0 :2-569_at_3HC :1_at_I2 density 0.015036
radial rdf1HO-I1.out 0.1 15.0 :2-569_at_1HO :1_at_I1 density 0.015036
radial rdf1HO-I2.out 0.1 15.0 :2-569_at_1HO :1_at_I2 density 0.015036

whereas the same simulation in moldy(http://www.ccp5.ac.uk/moldy/moldy.html)
I get a very gud radial distrubution function. my aim was to scale the
computing time of both the programs ..
could anyone help regarding this..

thanks in advance
prabhakar


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