Hi Hunter,
Well, that depends on the Amber version you're using, since the netcdf
fikes are outputted by default only from Amber14 (excluded) onwards.
To set them, you can just add to your input file the keyword "ioutfm=1",
that should output your minimization/dynamics in netcdf format.
Hope this is helpful.
Regards,
Manuele
Il mer 25 mar 2020, 18:11 Hunter Wilson <wils1872.umn.edu> ha scritto:
> Hey all,
>
> I'm currently struggling when writing my trajectory file outputs. I want
> them to be in the binary netcdf format, but they keep printing in the mdcrd
> format. Printed are my command line and input file. Any help is
> appreciated!
>
> Command:
> pmemd.cuda -O -i npt.in -o npt.out -p syrb12axno_NOG-F.prmtop -c
> syrb12axno_NOG-F_heat.rst -r syrb12axno_NOG-F_npt.rst -x
> syrb12axno_NOG-F_npt.nc
>
> Input:
> npt-density equilibration
> &cntrl
> imin=0,
> ntx=5,
> irest=1,
> nstlim=1000000,
> dt=0.002,
> ntf=2,
> ntc=2,
> temp0=300.0,
> ntpr=1000,
> ntwx=1000,
> ntwr=1000,
> cut=10.0,
> ntb=2,
> ntp=1,
> ntt=3,
> gamma_ln=2.0,
> nmropt=1,
> ig=-1,
> /
>
> Best,
> Hunter
> --
> Hunter Wilson
> Chemistry PhD Candidate
> Research Assistant
> Bhagi-Damodaran Group
> wils1872.umn.edu
>
> Department of Chemistry
> University of Minnesota- Twin Cities
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Received on Wed Mar 25 2020 - 10:30:02 PDT
