[gmx-users] Regarding Radial Distribution Functions

[Dilip H N]

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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> > <
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> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> >
> > 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.
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >   <https://mailtrack.io/> Sent with Mailtrack
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> > > referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > > > >
> > > > --
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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.