From: Ingrid Bernardes Santana Martins (ingrid.martins_at_unesp.br)
Date: Thu Dec 17 2020 - 13:18:23 CST
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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