From: Brian Radak (bradak_at_anl.gov)
Date: Thu Aug 18 2016 - 11:00:16 CDT
I've not used either of "measure rgyr" or "g_analyze", so I can only
assume they are correctly implemented.
I have pretty significant reservations about including your
equilibration components in the calculation. It's also not common to use
pressure control for these kinds of calculations, but I don't have a
specific reason as to why that's bad other than that it changes the
physical meaning of the result (I don't know what you want C(t) for, I
assume this is not a problem).
My guess is that you just have very poor statistics due to a long
characteristic time. This is not unexpected for a (presumably large)
system like a dendrimer.
Cheers,
Brian
On 08/18/2016 10:31 AM, faride badalkhani wrote:
> 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
> <mailto: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
>> <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 <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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