[gmx-users] Regarding Radial Distribution Functions

[Mark Abraham]

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&referral=cy16f01.dilip@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
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Research Scholar,
> Department of Chemistry, NITK.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>