From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Tue Aug 23 2016 - 13:59:31 CDT
How do you mean "correct"? Does the file execute successfully? It can be
very useful to try this and then read the INFO header lines.
NpT generally requires /more/ options than NVT. So long as you set
"langevin on" (or some other proper thermostat) and do not set
"langevinPiston on", you should get NVT results.
On 08/22/2016 07:34 AM, faride badalkhani wrote:
> Dear NAMD users,
>
> I want to perform a sequence of equilibration at NVT, then NPT, and
> then production at NPT. I have some questions:
> 1- I have never performed NVT simulations before, so could you tell me
> if the following configuration file is correct?
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # G5 OH terminated dendrimer in a Water Box
> # NVT ensemble
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ./OH-OH/input/OH_wb.psf
> coordinates ./OH-OH/input/OH_wb.pdb
>
> set temperature 300
> set outputname ./OH-OH/output/OH_eq
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ./OH-OH/input/par_all36_OH.prm
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.0
> switching on
> switchdist 10.0
> pairlistdist 14.0
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1 fs/step
> rigidBonds water ;# needed for 1 fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 73.5 0.0 0.0
> cellBasisVector2 0.0 86.5 0.0
> cellBasisVector3 0.0 0.0 88.4
> cellOrigin -12.7 -12.5 -26.3
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
>
>
> # let NAMD determine grid
> PMEGridSpacing 1.0
>
>
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
>
> # Output
> outputName $outputname
>
>
> restartfreq 5000 ;# 5000 steps = every 5.0 ps
> dcdfreq 5000
> xstFreq 5000
> outputEnergies 5000
> outputPressure 5000
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 20000
> reinitvels $temperature
>
> run 300000 ;# 300 ps
>
>
> 2- It would be necessary to set "rigidBonds water " when time
> step is 1 fs?
>
> 3- How many time steps are standard values for the first NVT and NPT
> simulations? (for example in Gromacs it is recommended to run NVT and
> NPT for 300 ps if someone wants to run the priduction run for 30 ns).
>
> Regards,
> Farideh
>
> On Thu, Aug 18, 2016 at 9:07 PM, Brian Radak <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> wrote:
>
> I would think the standard sequence is equilibrate at NpT, then
> NVT, and then production at NVT. Some people do things
> differently, and that's fine. There's nothing wrong with that - it
> just might be a bit slower (you could even check this during
> equilibration). It's up to you.
>
> Restarting probably shouldn't affect results. It might if you were
> trying to get very precise Newtonian dynamics, but there are
> plenty of other concerns in that case also.
>
>
> On 08/18/2016 11:31 AM, faride badalkhani wrote:
>>
>> 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 <mailto: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
>> <mailto: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
>>> <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 <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 Scholar Gordon Center for Integrative Science, W323A Department of Biochemistry & Molecular Biology University of Chicago 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 email: radak_at_uchicago.edu
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