I would output to netcdf files. Don't change 2 things at once if you are
having trouble. Make sure you can split them first, and then if desired do
the format conversion. It should work fine but if you have trouble it helps
to isolate the steps.
Concerning the box size, if you don't use box wrapping in the md, then they
will get large. This is not a problem since the system is periodic. It can
cause trouble for ascii formatted files with fixed precision, so you
probably want to image the coordinates back to the main box prior to saving
ascii format.
On Sun, Nov 12, 2023, 5:12 PM Singh,Ravi via AMBER <amber.ambermd.org>
wrote:
> Hello Carlos,
>
> To convert a file from .nc to mdcrd I use following cpptraj command
>
> trajin md.nc 1 10000 1
> trajout md.mdcrd crd
>
> Previosuly for other systems I received appropriate mdcrd files. However,
> upon increasing the size of system to 37500 atoms I have found weired
> cooridnates since box size is 75*75*75. The coordinates are not limited to
> the box size.
>
> Cpptraj Generated trajectory
> -416.730-101.326 -63.637-416.090-100.840 -62.850-416.804-100.678
> -64.539-416.217
> -102.181 -64.139-418.185-101.675 -63.175-418.079-102.236
> -62.258-418.574-102.283
> -63.949-419.059-100.475 -62.950-418.942 -99.856 -63.824-418.632 -99.829
> -61.775
> -417.848 -99.261 -61.895-420.581-100.802 -62.843-420.865-100.998
> -61.806-421.155
> -99.857 -62.993-420.970-101.527 -63.589 -50.998 -82.641 809.933 -51.440
> -83.007
> 808.977 -51.467 -81.702 809.972 -51.498 -83.283 810.656 -49.496 -82.612
> 810.096
>
> What could be a possible solution for the conversion to .mdrcrd file??
>
>
> Your help will be highly appreciated
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>
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Received on Sun Nov 12 2023 - 14:30:04 PST
