Since you have the same value for all of your ntws (500) you can use ntwf =
500.
There are other options you can use as well, such as ntwf=- 1.
Please read page 322 in the amber manual. see link here.
http://ambermd.org/doc12/Amber18.pdf
On Sun, Jun 24, 2018 at 4:46 PM Lod King <lodking407.gmail.com> wrote:
> Thank you.
>
> Below is my parameter for a 10ms run.. it seems like I did not set up for
> "ntwf"..
>
> mplict_water
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> mplict_water
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 5,
> ioutfm = 1,
> nstlim = 5000000,
> dt = 0.002,
> ntt = 3,
> gamma_ln = 2.0,
> ig = -1,
> tempi = 300.0,
> temp0 = 300.0,
> ntp = 1,
> ntb = 2,
> ntc = 2,
> ntf = 2,
> cut = 12,
> ntwr = 500,
> ntpr = 500,
> ntwx = 500,
> ntwe = 500,
> iwrap = 1,
> ntr = 0,
> /
> $ewald
> nfft1=128,
> nfft2=108,
> nfft3=96,
> order=4,
> /
>
> if I am going to add this parameter in my input file, what value should I
> put? default or any data I can refer to?
>
> On Sun, Jun 24, 2018 at 1:18 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Sun, Jun 24, 2018, Lod King wrote:
> > >
> > > I would like to extract the force for each atom in a 100ns run
> > trajectory.
> > >
> > > I have a folder containing:
> > >
> > > prmtop file
> > > dcd file (combined from 10 mdcrd files, each 10ns)
> > > 10 mdcrd files
> > >
> >
> > Do these files contain forces, or coordinates? That is, how did you
> > create the mdcrd files? If you didn't set the "ntwf" parameter, your
> > mdcrd files will just contain coordinates, and you cannot extract forces
> > from these.
> >
> > If you did use ntwf, then you have the forces for each atom, at each
> > time step that was saved. You can load this as a "dataset" into
> > cpptraj, and use its commands to perform various types of analysis, such
> > as averages, time-correlation functions, etc. If you need some other
> > type of analysis, you will need to write your own scripts to analyze the
> > data: pytraj can help a lot if you are comfortable using that language.
> >
> > ...hope this helps....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Jun 24 2018 - 18:00:03 PDT
