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
>
>
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Received on Sun Jun 24 2018 - 14:00:03 PDT
