From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Aug 18 2016 - 10:31:53 CDT
This system is a Dendrimer, which is a hyperbranched polymer. I used the
following script to calculate the radius of gyration:
set outfile [open rg.dat w]
set mol [molinfo top]
set sel [atomselect top "all not waters"]
set frames [molinfo $mol get numframes]
for {set i 0} {$i < $frames} {incr i} {
$sel frame $i
$sel update
puts $outfile "$i [measure rgyr $sel]"
}
close $outfile
$sel delete
For calculating the C(t) I used the g_analyze in gromacs and the Rg
computed using the above script. for plotting the data I used the whole
simulation time (40 ns). I loaded all the trajectory files in VMD and then
calculated the Rg.
Regards,
Farideh
On Thu, Aug 18, 2016 at 7:51 PM, Brian Radak <bradak_at_anl.gov> wrote:
> 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> 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
>>
>
>
> --
> 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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