Re: Polymer moves to the edge of water box during the simulation

From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Apr 14 2016 - 09:56:07 CDT

Hi,

I need to know what is the best way to construct the initial structure in
the best way for a polymer, which there is no pdb file for?

Regards,
Farideh

On Wed, Apr 13, 2016 at 10:25 PM, faride badalkhani <
farideh.khamseh_at_gmail.com> wrote:

> Hi,
>
> Thanks for introducing the link. Since there is no crystallographic data
> for my structure (hyperbranched polymers) I built the pdb file and then I
> performed the following steps:
> 1) Simulated annealing for the structure in vacuum from 300-700 and vice
> versa, system remained in each step for 50 ps and after that MD simulation
> for 1 ns
>
> 2) minimizing the system and water box for 25 ps followed by 100 ps MD in
> NPT ensemble while rigid bonds was set to all
>
> 3) minimizing the system and water box for 25 ps followed by 100 ps MD in
> NPT ensemble while rigid bonds was set to water
>
> 4) performing MD simulation for 600 ps in NPT
>
> but when I want to perform production MD I get error.
> p.s. according to
>
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/1163.html
> I added |MINx| + |MAXx|, |MINy| + |MAXy|, |MINz| + |MAXz| to determine
> cell basis vectorsx, y, and z.
> and all these simulations were performed with 0.5 fs time step.
>
> Regards,
> Farideh
>
> On Wed, Apr 13, 2016 at 6:02 PM, faride badalkhani <
> farideh.khamseh_at_gmail.com> wrote:
>
>> Hi,
>>
>> Thanks for introducing the link. Since there is no crystallographic data
>> for my structure (hyperbranched polymers) I built the pdb file and then I
>> performed the following steps:
>> 1) Simulated annealing for the structure in vacuum from 300-700 and vice
>> versa, system remained in each step for 50 ps and after that MD simulation
>> for 1 ns
>>
>> 2) minimizing the system and water box for 25 ps followed by 100 ps MD in
>> NPT ensemble while rigid bonds was set to all
>>
>> 3) minimizing the system and water box for 25 ps followed by 100 ps MD in
>> NPT ensemble while rigid bonds was set to water
>>
>> 4) performing MD simulation for 600 ps in NPT
>>
>> but when I want to perform production MD I get error.
>> p.s. according to
>>
>> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/1163.html
>> I added |MINx| + |MAXx|, |MINy| + |MAXy|, |MINz| + |MAXz| to determine
>> cell basis vectorsx, y, and z.
>> and all these simulations were performed with 0.5 fs time step.
>>
>> Regards,
>> Farideh
>>
>> On Wed, Apr 13, 2016 at 9:02 AM, Josh Vermaas <vermaas2_at_illinois.edu>
>> wrote:
>>
>>> Yes, make your system more stable or increase the size of the
>>> pairlistdist or cutoff. I'm used to seeing 1 or 2 fs/step. 0.5 will of
>>> course work, but it seems like a band-aid solution to a larger structural
>>> problem. How long was the system minimized prior to simulation? Are there
>>> any atoms initially at 0, 0, 0? Those are the kinds of questions you should
>>> be asking yourself. See
>>> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_namd_wiki_index.cgi-3FNamdTroubleshooting&d=BQMDaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=soZTpEoxMxlkKr6CfyPMONjlHTcyVdhBXRwv_LBhk7Y&m=kObCFU9WTKdBrqxw4IWPhBJ__jGVBhGAMD0rLV2zR30&s=6E6EFUvVDwaaUOlfzJxQeVi1M57lkNt0ROKp-k7cMGM&e=>
>>> -Josh
>>>
>>>
>>> On 04/12/2016 05:02 PM, faride badalkhani wrote:
>>>
>>> Hi,
>>>
>>> My configuration file is as follows:
>>>
>>> ############################################################
>>> ## JOB DESCRIPTION ##
>>> #############################################################
>>>
>>> # Equilibration of G5 Alkyne OH terminated
>>> # dendron in a Water Box
>>>
>>>
>>> #############################################################
>>> ## ADJUSTABLE PARAMETERS ##
>>> #############################################################
>>>
>>> structure Alkyne-NPT/Alkyne_OH_wb.psf
>>> coordinates Alkyne-NPT/Alkyne_OH_wb.pdb
>>>
>>> set temperature 300
>>> set outputname Al_OH_NPT
>>>
>>> # Continuing a job from the restart files
>>> if {1} {
>>> set inputname Al_300_eq ;# only need to edit
>>> this in one place!
>>> binCoordinates $inputname.restart.coor ;# coordinates from last
>>> run (binary)
>>> binVelocities $inputname.restart.vel ;# velocities from last
>>> run (binary) ;# remove the "temperature" entry if you use this!
>>> extendedSystem $inputname.restart.xsc ;# cell dimensions
>>> from last run
>>> }
>>>
>>> firsttimestep 0
>>>
>>>
>>> #############################################################
>>> ## SIMULATION PARAMETERS ##
>>> #############################################################
>>>
>>> # Input
>>> paraTypeCharmm on
>>> parameters Alkyne-NPT/par_all36_prot.prm
>>> parameters Alkyne-NPT/par_all36_Alkyne.prm
>>>
>>> # NOTE: Do not set the initial velocity temperature if you
>>> # have also specified a .vel restart file!
>>> # temperature $temperature
>>>
>>> # Force-Field Parameters
>>> exclude scaled1-4 ;# These are specified by CHARMM
>>> 1-4scaling 1.0 ;# These are specified by CHARMM
>>> cutoff 12.0 ;# may use smaller, maybe 10.0, with PME
>>> switching on
>>> switchdist 10.0 ;# cutoff - 2.0
>>> pairlistdist 14.0 ;# Promise that atom won’t move more
>>> than 2A in a cycle, cutoff + 2
>>>
>>>
>>> # Integrator Parameters
>>> timestep 0.5 ;# 0.5 fs/step
>>> rigidBonds water
>>> nonbondedFreq 1 ;# nonbonded forces every step
>>> fullElectFrequency 2 ;# PME only every other step
>>> stepspercycle 10 ;# redo pairlists every ten steps
>>>
>>>
>>> # 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
>>> # NOTE: Do not set the periodic cell basis if you have also
>>> # specified an .xsc restart file!
>>> if {0} {
>>> cellBasisVector1 49.14 0.00 0.00
>>> cellBasisVector2 0.00 91.77 0.00
>>> cellBasisVector3 0.00 0.00 52.44
>>> cellOrigin -1.97 45.97 1.42
>>> }
>>> wrapWater on ;# wrap water to central cell
>>> wrapAll on ;# wrap other molecules too
>>> wrapNearest off ;# use for non-rectangular cells
>>>
>>> # PME (for full-system periodic electrostatics)
>>> if {1} {
>>> PME yes
>>>
>>> # let NAMD determine grid
>>> PMEGridSpacing 1.0
>>> }
>>>
>>> # Constant Pressure Control (variable volume)
>>> useGroupPressure yes ;# needed for rigidBonds
>>> useFlexibleCell no
>>> useConstantArea no
>>>
>>> langevinPiston on
>>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>>> langevinPistonPeriod 100.0
>>> langevinPistonDecay 50.0
>>> langevinPistonTemp $temperature
>>>
>>> # Output
>>> outputName $outputname
>>>
>>> restartfreq 1000 ;# 1000 steps = every 0.5 ps
>>> dcdfreq 500
>>> xstFreq 500
>>> outputEnergies 200
>>> outputPressure 200
>>> outputTiming 1000 ;# shows time per step and time to completion
>>>
>>> #############################################################
>>> ## EXTRA PARAMETERS ##
>>> #############################################################
>>>
>>> margin 5
>>>
>>> #############################################################
>>> ## EXECUTION SCRIPT ##
>>> #############################################################
>>>
>>> run 1200000 ;# 600 ps
>>>
>>>
>>> and I have one more question. I do not get error just when consider time
>>> step as 0.5 fs. When I set the time step 1.0 fs I get this error
>>> Low global CUDA exclusion count! (13856 vs 13858) System unstable or
>>> pairlistdist or cutoff too small.
>>> Do you think is there any way to prevent this error?
>>>
>>> Regards,
>>> Farideh
>>>
>>> On Tue, Apr 12, 2016 at 5:54 PM, Josh Vermaas <vermaas2_at_illinois.edu>
>>> wrote:
>>>
>>>> Hi Farideh,
>>>>
>>>> Why is this a problem? Things move in simulation. That's kinda the
>>>> point. :D What are your wrapping options? Odds are you have wrap water or
>>>> wrap all turned on, and you are getting thrown because it isn't wrapping
>>>> like you expect.
>>>>
>>>> -Josh
>>>>
>>>>
>>>> On 04/12/2016 04:49 PM, faride badalkhani wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I am performing a NPT simulation for a hyperbranched polymer in water
>>>> box. There is no error message but when I load trajectory file I see that
>>>> the polymer moves to the edge of water box. Could you tell me please what
>>>> is the problem?
>>>> Any help will be appreciated.
>>>>
>>>> Regards,
>>>> Farideh
>>>>
>>>>
>>>>
>>>
>>>
>>
>

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