From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Aug 18 2016 - 10:16:34 CDT
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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