[gmx-users] Regarding Radial Distribution Functions

[Dilip H N]

and how it has influence on rdf..??



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On Mon, Mar 20, 2017 at 11:24 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
wrote:

> Can u kindly let me knw where can i get the information of collection rate
> and correlation time.??
>
>
>
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> On Mon, Mar 20, 2017 at 10:54 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Well gmx rdf has a -bin option for you to get a feel for where your
>> existing data supports smoothness. But I literally can't know what your
>> data's correlation time and collection rate are :-)
>>
>> Mark
>>
>> On Mon, 20 Mar 2017 18:18 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>>
>> > So where should i look into..?? 1st i made the indexes, than gave gmx
>> rdf
>> > command with -f .trr -s .tpr files, and thn output for the rdf...
>> > What other things should i look for..??
>> >
>> >
>> >
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>> > >
>> >
>> > On Mon, Mar 20, 2017 at 10:41 PM, Mark Abraham <
>> mark.j.abraham at gmail.com>
>> > wrote:
>> >
>> > > Hi,
>> > >
>> > > You're making a histogram. The size of the bins and the number of
>> > > statistically independent data points in each bin are critical
>> parameters
>> > > in how smooth that looks.
>> > >
>> > > Mark
>> > >
>> > > On Mon, 20 Mar 2017 17:00 Dilip H N <cy16f01.dilip at nitk.edu.in>
>> wrote:
>> > >
>> > > > Hello.,
>> > > > I ran a simultion for 10ns [ steps = 10000000, dt = 0.002] and whn i
>> > > index
>> > > > the file and thn if i plot the rdf , the rdf curves are not smooth,
>> > there
>> > > > are lot of peaks present, and even after runnig the steps for more
>> no
>> > of
>> > > > steps ie., for 20ns and after tht also my rdf peaks are not so
>> > > smooth...why
>> > > > is this so..?? How can i smoothen my curve..??
>> > > >
>> > > > --
>> > > > With Best Regards,
>> > > >
>> > > > DILIP.H.N
>> > > > Research Scholar,
>> > > > Department of Chemistry, NITK.
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
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>> > > > >
>> > > > --
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>> >
>> > --
>> > With Best Regards,
>> >
>> > DILIP.H.N
>> > Research Scholar,
>> > Department of Chemistry, NITK.
>> > --
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>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
>



-- 
With Best Regards,

DILIP.H.N
Research Scholar,
Department of Chemistry, NITK.