Re: Autocorrelation function of Rg goes down without fluctuation around zero

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Aug 18 2016 - 11:31:05 CDT

And I have one more questions! Could you tell me if the restarting the
simulations every 5 ns affects the results or not?

Regards,
Farideh

On Aug 18, 2016 8:57 PM, "faride badalkhani" <farideh.khamseh_at_gmail.com>
wrote:

> So, do you think it is more reasonable to perform minimization and then
> NVT simulation for a few time steps before production run?
>
> Regards,
> Farideh
>
> On Aug 18, 2016 8:50 PM, "Brian Radak" <bradak_at_anl.gov> wrote:
>
>> After equilibration to a desired density, pressure control is usually
>> just an added cost (maybe 5-10%?) with not much value. I usually do
>> everything at NVT. For equilibration at the force field density, these are
>> usually indistinguishable (unless you want temperature or pressure
>> dependent properties).
>> On 08/18/2016 11:16 AM, faride badalkhani wrote:
>>
>> Usually, the autocorrelation function of Rg is used to find if the
>> structure is well equilibrated or not, and to find relaxation time for
>> them.
>> What do you mean with "It's also not common to use pressure control for
>> these kinds of calculations"? Which method do you suggest for perfotming
>> simulations?
>>
>> Regards,
>> Farideh
>>
>> On Aug 18, 2016 8:30 PM, "Brian Radak" <bradak_at_anl.gov> wrote:
>>
>>> 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> 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-dJEEx0SBl
>>>> U2Fuekma?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
>>>>
>>>
>>>
>>> --
>>> 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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