For one thing, you're not passing a topology file in based on what you gave
us - where's the .prmtop in all of this?
Also, you might be seeing the effects of the system wandering in and out of
the periodic boundaries, did you specify wrapping?
T
On Sun, Nov 12, 2023 at 4:12 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 - 14:30:03 PST
