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

Date: Fri Aug 19 2016 - 04:00:59 CDT

So, do you think how can I find that the structure is well equilibrated?
(maybe using RMSD?) Did you find something wrong with the RMSD and Rg?

The problem is that I performed the same simulations for another type of
dendrimers (PAMAM dendrimers) and I got a reasonable correlation function.
But in this case (Polyester dendrimers) I could not get the correlation
function, though I performed the simulation for PAMAM for 27 ns but for the
latter one for 40 ns.

Regards,
Farideh

On Fri, Aug 19, 2016 at 11:12 AM, Lennart Nilsson <Lennart.Nilsson_at_ki.se>
wrote:

> You may need close to a microsecond to get this to converge; there seems
> to be a slow component with a correlation time of at least 20 ns. There is
> usually no point in plotting a correlation function for more than about 1/3
> of the length of the underlying time-series, and a rule-of-thumb is that
> your trajectory has to be at least 10x the correlation time of the property
> of interest in order to get a reasonable correlation function.
>
>
>
> Best,
>
> Lennart
>
>
>
>
>
>
>
> *Sent:* den 18 augusti 2016 20:50
> *To:* Lennart Nilsson <Lennart.Nilsson_at_ki.se>
> *Cc:* namd-l_at_ks.uiuc.edu
>
> *Subject:* Re: namd-l: Autocorrelation function of Rg goes down without
> fluctuation around zero
>
>
>
> Hi,
>
>
>
> I am sorry! You are right I had forgotten to add it. You can find it in
>
>
>
>
>
>
> 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
> *Sent:* den 18 augusti 2016 17:17
> *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:
>
>
> 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:
>
> 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
>
>
>
> --
> Postdoctoral Appointee