From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Fri Dec 18 2020 - 07:52:09 CST
Your dcdfreq is 100. Take a look at the user guide as to what this means,
but if the simulation fully completed without running out of time on a
supercomputer or crashing, the number of frames is deterministic.
Josh
On Fri, Dec 18, 2020, 6:41 AM Mi Yang <drmiyang2019_at_gmail.com> wrote:
> Dear Martins,
> Thanks for your reply. Yes, my estimation was also the same but it is
> confirmed now.
> Just one more thing, do you know any link to guess expected No. frames of
> trajectory over a given time as above. or it is always random No?
>
>
> On Thu, Dec 17, 2020 at 10:18 PM Ingrid Bernardes Santana Martins <
> ingrid.martins_at_unesp.br> wrote:
>
>> If you have *30000000* steps of *1* fs, you need to multiply
>> *30000000x1*10^-15* s
>> That will be 30x10^-9 s, or 30 ns
>>
>> Em qui., 17 de dez. de 2020 às 15:56, Mi Yang <drmiyang2019_at_gmail.com>
>> escreveu:
>>
>>> Dear Colleagues,
>>> I am running NAMD calculation with the following config. Can anyone help
>>> me to assess time for total run: How calculate it?
>>> .config
>>> # ----------output------
>>>
>>> set output output
>>>
>>> outputname $output
>>> dcdfile ${output}.dcd
>>> xstFile ${output}.xst
>>> dcdfreq 100
>>> xstFreq 100
>>> binaryoutput yes
>>> binaryrestart yes
>>> outputEnergies 100
>>> restartfreq 100
>>>
>>>
>>> # ---------Basic dynamics-------
>>> exclude scaled1-4
>>> 1-4scaling 1
>>> COMmotion no
>>> dielectric 1.0
>>>
>>> # --------Simulation space partitioning----
>>> switching on
>>> switchdist 9
>>> cutoff 10
>>> pairlistdist 11
>>>
>>> # --------Multiple time stepping----
>>> firsttimestep 0
>>> *timestep 1*
>>> stepspercycle 1
>>>
>>> # -------Temperature control----
>>> set temperature 310
>>> temperature $temperature; # initial temperature
>>>
>>> # -------Langevin Dynamics------
>>> langevin on; # do langevin dynamics
>>> langevinDamping 1; # damping coefficient (gamma) of
>>> 1/ps
>>> langevinTemp $temperature; # bath temperature
>>>
>>> # ===============================================
>>>
>>> PME on
>>> PMEGridSizeX 100
>>> PMEGridSizeY 100
>>> PMEGridSizeZ 100
>>>
>>> # doesnt work with just pme
>>>
>>> useGroupPressure yes
>>>
>>> # with grouppressure, works better, holes still there
>>>
>>> LangevinPiston on
>>> LangevinPistonTarget 1.02
>>> LangevinPistonPeriod 150
>>> LangevinPistonDecay 90
>>> LangevinPistonTemp $temperature
>>>
>>> # with langevin piston, works!!! But slower.
>>>
>>> # ===============================================
>>>
>>> # Periodic Boundary conditions
>>> cellBasisVector1 61.78700256347656 0 0
>>> cellBasisVector2 0 50.00300121307373 0
>>> cellBasisVector3 0 0 56.50100135803223
>>> cellOrigin 42.02330017089844 -13.173894882202148 16.507816314697266
>>>
>>> wrapWater on ;# wrap water to central cell
>>> wrapAll on ;# wrap other molecules too
>>> wrapNearest off
>>>
>>> # ---------Scripting
>>> minimize 1000 ;# lower potential energy for 10000
>>> steps
>>> reinitvels $temperature ;# since minimization zeros velocities
>>> *run 30000000;*
>>>
>>> # END
>>>
>>
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