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.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.C1 :1.I1 density 0.015036
>> > radial rdfC1-I2.out 0.1 15.0 :2-569.C1 :1.I2 density 0.015036
>> > radial rdfO1-I1.out 0.1 15.0 :2-569.O1 :1.I1 density 0.015036
>> > radial rdfO1-I2.out 0.1 15.0 :2-569.O1 :1.I2 density 0.015036
>> > radial rdf1HC-I1.out 0.1 15.0 :2-569.1HC :1.I1 density 0.015036
>> > radial rdf1HC-I2.out 0.1 15.0 :2-569.1HC :1.I2 density 0.015036
>> > radial rdf2HC-I1.out 0.1 15.0 :2-569.2HC :1.I1 density 0.015036
>> > radial rdf2HC-I2.out 0.1 15.0 :2-569.2HC :1.I2 density 0.015036
>> > radial rdf3HC-I1.out 0.1 15.0 :2-569.3HC :1.I1 density 0.015036
>> > radial rdf3HC-I2.out 0.1 15.0 :2-569.3HC :1.I2 density 0.015036
>> > radial rdf1HO-I1.out 0.1 15.0 :2-569.1HO :1.I1 density 0.015036
>> > radial rdf1HO-I2.out 0.1 15.0 :2-569.1HO :1.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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Received on Fri Dec 12 2008 - 01:09:11 PST
