From: Brian Radak (bradak_at_anl.gov)
Date: Thu Aug 18 2016 - 10:21:30 CDT
What system is this? How did you compute Rg and C(t)? Which parts of the
trajectory were used?
Correlation functions can be very slow to converge, 5 ns might not be
enough.
On 08/18/2016 10:16 AM, faride badalkhani wrote:
> 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>
>
>
-- 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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