Dear both,
Yeah, that's right. This is a trajectory from the minimization.
cell_lengths variable is there when running "$ ncdump -h trajectory.mdcrd":
double cell_lengths(frame, cell_spatial) ;
cell_lengths:units = "angstrom" ;
So, there is actually something wrong in reading the trajectory in cpptraj.
Is there any way I can add the box to the trajectory.mdcrd, and thus start
the MD with such new box?
Also, will it generate unphysical issues, like self-interactions, due to
the different PBC?
Cheers,
Manuele
Il giorno ven 22 mag 2020 alle ore 13:32 David A Case <
david.case.rutgers.edu> ha scritto:
> On Fri, May 22, 2020, Dan Roe wrote:
> >
> >Is trajectory.mdcrd the trajectory file from the QM/MM simulation? Double
> >check that box info is there with ‘ncdump -h’ and look for the variable
> >cell_lengths. If it isn’t there then for some reason box info wasn’t
> >written to the trajectory file. If it is there, cpptraj is missing the
> info
> >somehow.
>
> Just a note: this is a "trajectory" file from a minimization run, not
> from MD. It could be that there is something odd about that code path,
> which is rarely used, and probably not tested.
>
> ....dac
>
>
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*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
w: http://tompenfoldresearch.weebly.com/
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Received on Fri May 22 2020 - 07:00:02 PDT
