From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Aug 18 2016 - 11:27:39 CDT
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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