Re: [AMBER] QM/MM MD: Error reading box

From: emanuele falbo <>
Date: Fri, 22 May 2020 14:58:27 +0100

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?


Il giorno ven 22 mag 2020 alle ore 13:32 David A Case <> 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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> AMBER mailing list

*Emanuele Falbo*
PhD student
Penfold group
School of Natural and Environmental Sciences
Bedson Building, Newcastle University
Newcastle upon Tyne, NE1 7RU
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Received on Fri May 22 2020 - 07:00:02 PDT
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