**From:** faride badalkhani (*farideh.khamseh_at_gmail.com*)

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

**Next message:**Brian Radak: "Re: how to rerun a namd trajectory in order to complement the missing snapshots?"**Previous message:**Lennart Nilsson: "RE: Autocorrelation function of Rg goes down without fluctuation around zero"**In reply to:**Lennart Nilsson: "RE: Autocorrelation function of Rg goes down without fluctuation around zero"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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
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*> your trajectory has to be at least 10x the correlation time of the property
*

*> of interest in order to get a reasonable correlation function.
*

*>
*

*>
*

*>
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*> Best,
*

*>
*

*> Lennart
*

*>
*

*>
*

*>
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*>
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*>
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*>
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*>
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*> *From:* faride badalkhani [mailto:farideh.khamseh_at_gmail.com]
*

*> *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
*

*> 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
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*> itself? There is no reason for <Rg(t)Rg(t+T)> to decay to zero; quite the
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*> opposite.
*

*>
*

*> I did not find C(t) in the files you posted, only Rg(t).
*

*>
*

*> Best,
*

*>
*

*> Lennart
*

*>
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*>
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*>
*

*> *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
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*> 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
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*> paramchem.
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*>
*

*> 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
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*> 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
*

*>
*

*>
*

*>
*

*>
*

*>
*

**Next message:**Brian Radak: "Re: how to rerun a namd trajectory in order to complement the missing snapshots?"**Previous message:**Lennart Nilsson: "RE: Autocorrelation function of Rg goes down without fluctuation around zero"**In reply to:**Lennart Nilsson: "RE: Autocorrelation function of Rg goes down without fluctuation around zero"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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