AMBER Archive (2008)Subject: Re: AMBER: Radial Distribution Function
From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Dec 10 2008  07:49:42 CST
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 CI and OI 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 photodissociation.
>> > 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 rdfC1I1.out 0.1 15.0 :2569_at_C1 :1_at_I1 density 0.015036
>> > radial rdfC1I2.out 0.1 15.0 :2569_at_C1 :1_at_I2 density 0.015036
>> > radial rdfO1I1.out 0.1 15.0 :2569_at_O1 :1_at_I1 density 0.015036
>> > radial rdfO1I2.out 0.1 15.0 :2569_at_O1 :1_at_I2 density 0.015036
>> > radial rdf1HCI1.out 0.1 15.0 :2569_at_1HC :1_at_I1 density 0.015036
>> > radial rdf1HCI2.out 0.1 15.0 :2569_at_1HC :1_at_I2 density 0.015036
>> > radial rdf2HCI1.out 0.1 15.0 :2569_at_2HC :1_at_I1 density 0.015036
>> > radial rdf2HCI2.out 0.1 15.0 :2569_at_2HC :1_at_I2 density 0.015036
>> > radial rdf3HCI1.out 0.1 15.0 :2569_at_3HC :1_at_I1 density 0.015036
>> > radial rdf3HCI2.out 0.1 15.0 :2569_at_3HC :1_at_I2 density 0.015036
>> > radial rdf1HOI1.out 0.1 15.0 :2569_at_1HO :1_at_I1 density 0.015036
>> > radial rdf1HOI2.out 0.1 15.0 :2569_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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