From: Brian Radak (bradak_at_anl.gov)
Date: Thu Aug 18 2016 - 11:20:22 CDT
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
> <mailto: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
>> <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 <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
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:23 CST