From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Wed Apr 13 2016 - 12:55:28 CDT
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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