Re: Autocorrelation function of Rg goes down without fluctuation around zero

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Aug 18 2016 - 13:50:23 CDT

Hi,

I am sorry! You are right I had forgotten to add it. You can find it in the
link below:

https://www.dropbox.com/sh/mcnkxt9pefnqgrz/AADRRw4-dJEEx0SBlU2Fuekma?dl=0

In the case of dendrimers usually the equilibrium behavior of the
dendrimers is determined via the autocorrelation function of the Rg (CRg),
cross crosscorrelation
of time course of Rg with itself. And, according to literature if the
autocorrelation function fluctuate around zero it means that the overall
structure is well equilibrated.
I did not know how to calculate C Rg(t) in NAMD and did not have a script
so, I used the g_analyze command in gromacs.

Regards,
Farideh

On Thu, Aug 18, 2016 at 10:59 PM, Lennart Nilsson <Lennart.Nilsson_at_ki.se>
wrote:

> Are you sure that you have calculated the autocorrelation < (Rg(t) -
> <Rg>)(Rg(t+T)-<Rg>)>, ie of the Rg **fluctuations**, and not of Rg
> itself? There is no reason for <Rg(t)Rg(t+T)> to decay to zero; quite the
> opposite.
>
> I did not find C(t) in the files you posted, only Rg(t).
>
> Best,
>
> Lennart
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *faride badalkhani
> *Sent:* den 18 augusti 2016 17:17
> *To:* Brian Radak <bradak_at_anl.gov>
> *Cc:* namd-l <namd-l_at_ks.uiuc.edu>
> *Subject:* Re: namd-l: Autocorrelation function of Rg goes down without
> fluctuation around zero
>
>
>
> Thank you for your answer and time. At first I performed minimization for
> 20 ps and then NPT simulation for 10 ns. After that, I restarted the
> simulation for 5 more ns and continued simulation in 5 ns steps till 40 ns.
> I did not get any error during the simulations, but the autocorrelation
> function does not fluctuate around zero. I have shared the Rg, RMSD, and
> C(t) ans also .top, .par, .conf, .pdb, and the .log file for the first 10
> ns in the link below:
>
> https://www.dropbox.com/sh/mcnkxt9pefnqgrz/AADRRw4-dJEEx0SBlU2Fuekma?dl=0
>
> p.s. Bond distances, angles, dihedrals and impropers were taken form
> CHARMM GENERAL FORCE FIELD and the charges were assigned using CGen FF on
> paramchem.
>
> Thank you so much for your help!
>
> Regards,
>
> Farideh
>
>
>
> On Thu, Aug 18, 2016 at 7:17 PM, Brian Radak <bradak_at_anl.gov> wrote:
>
> You either made a mistake in your calculation or else your statistics are
> bad. Some details might help distinguish which of those is the case.
>
> HTH,
> Brian
>
>
>
> On 08/18/2016 04:21 AM, faride badalkhani wrote:
>
> Dear NAMD users,
>
> I have plotted the autocorrelation function of radius of gyration as a
> function of time to investigate the equilibration of a system of
> hyperbranched polymer. However, the plot goes down and does not fluctuate
> around zero.
>
> Could anybody tell me what is the reason and what should I do?
> Any help will be appreciated.
>
> Regards,
> Farideh
>
>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
>
>
>

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