AMBER Archive (2008)

Subject: Re: AMBER: Radial Distribution Function

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Dec 09 2008 - 09:38:54 CST

Hi there,

Could you check your ptraj output for the results of the atom
selection masks you are using? That is output in the begginign og the
ptraj output file.

The plot you show only has 3 distinctive sets of lines: The first two
come from the C-I and O-I RDFs, and the last set is uncertain, but
probably bunches together everything that contain Hydrogens. My guess
is that ptraj is not completely understanding your selection masks
when it comes to the Hydrogens.

Gustavo.

On Mon, Dec 8, 2008 at 9:37 PM, prabhakar g wrote:
> 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
> 

-- 
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu