AMBER Archive (2008)

Subject: Re: AMBER: Radial Distribution Function

From: prabhakar g (prabha.kaist_at_gmail.com)
Date: Fri Dec 12 2008 - 20:31:48 CST

Moldy is another molecular dynamics code that is use to do simulation,
here is the link http://www.ccp5.ac.uk/moldy/moldy.html

prabhakar

On Wed, Dec 10, 2008 at 10:49 PM, Gustavo Seabra
<gustavo.seabra_at_gmail.com>wrote:

> It may be more helpful if you can tell us exactly what you mean by the
> "moldy simulations". Do you have an example to show? How do you plot
> the RDFs you are comparing to? Are you sure they use exactly the same
> parameters as you are using in ptraj? (spacing, density, etc)?
>
> Gustavo.
>
> On Tue, Dec 9, 2008 at 10:33 PM, prabhakar g wrote:
> > Thank you Dr.Gustavo. I checked and corrected the names of the hydrogen
> > verifying it from leap and got it fixed. now all the RDFs pairs are
> > converging to 1. But I find that the RDF curve is very noisy( am saving
> the
> > coordinate every 200fs and the time step is 0.5fs), when compared to that
> of
> > moldy simulations, any suggestions.?
> >
> > regards
> > prabhakar
> >
> > On Wed, Dec 10, 2008 at 12:38 AM, Gustavo Seabra <
> gustavo.seabra_at_gmail.com>
> > wrote:
> >>
> >> 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
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