From: Mi Yang (drmiyang2019_at_gmail.com)
Date: Fri Dec 18 2020 - 07:38:23 CST
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
>>
>
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:10 CST