[gmx-users] Regarding Radial Distribution Functions

[Mark Abraham]

Hi,

You already chose your data collection rate in your mdp file. Your
correlation time depends  on the physics (no point collecting data more
often than this, so just using nstxout=1 is bogus). And I'm sure google is
your friend for learning about basic concepts of histograms and bin width.

Mark

On Mon, 20 Mar 2017 18:56 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> and how it has influence on rdf..??
>
>
>
>   <https://mailtrack.io/> Sent with Mailtrack
> <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
>
> 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.??
> >
> >
> >
> >   <https://mailtrack.io/> Sent with Mailtrack
> > <
> https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.dilip@nitk.edu.in&idSignature=22
> >
> >
> > 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..??
> >> >
> >> >
> >> >
> >> >   <https://mailtrack.io/> Sent with Mailtrack
> >> > <
> >> > https://mailtrack.io/install?source=signature&lang=en&referr
> >> al=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
> >> > > > <
> >> > > > https://mailtrack.io/install?source=signature&lang=en&
> >> > > 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.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
> --
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