This works great! Thank you for your help!
On Wed, Mar 25, 2020 at 12:17 PM emanuele falbo <falbo.emanuele.gmail.com>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 12:30:03 PDT
