Re: Using PBC tools for a cubic and a rectangular box

From: Monika Madhavi (
Date: Wed Mar 28 2018 - 23:07:41 CDT

Dear all,

Thank you for you insights into the problem. I tested pbc get -all command.
It extracts the correct unit cell from each DCD frame, without specifying
any other information. The problem still remains the same.


On Tue, Mar 27, 2018 at 7:48 PM, Giacomo Fiorin <>

> I can't say for sure. Also, I haven't tried with NetCDF files, although
> they may work because molfile does support unit cell I/O.
> For sure the fact that a DCD file was created with NAMD is not sufficient
> to know whether it'll work: it depends on the value of DCDUnitCell, and on
> the presence of PBCs. NAMD sets internally a { 1 1 1 90 90 90 } unit cell
> when PBCs are not enabled to avoid divisions by zero, but this may end up
> in unexpected behavior once the files are loaded in VMD.
> Giacomo

W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.

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