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

From: Monika Madhavi (monikamadhavi_at_gmail.com)
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.

Best,
Monika

On Tue, Mar 27, 2018 at 7:48 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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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