From: Lennart Nilsson (Lennart.Nilsson_at_ki.se)
Date: Fri Aug 19 2016 - 01:42:03 CDT
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
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<mailto: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> [mailto: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<mailto:bradak_at_anl.gov>>
Cc: namd-l <namd-l_at_ks.uiuc.edu<mailto: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<mailto: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<mailto:brian.radak_at_anl.gov>
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