[gmx-users] (no subject)

[Dd H]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Have a look at this, hope it's helpful.

Dading Huang

On Sat, Nov 19, 2016 at 1:36 PM, Kingsley Theras Primus Dass . <
105726107 at gms.tcu.edu.tw> wrote:

> Dear Users!!
>
>
>  I have a question about RMSD.  I ran MＤ simulaton for 500ns and connected
> all my .xtc files using trjcat command.
> And , then I used g_rms command with the connected .xtc file to calculate
> RMSD for backbone atoms. But , when I run g_rms command , I get a warning
> as follows:
>
>
>
> WARNING: If there are molecules in the input trajectory file
>          that are broken across periodic boundaries, they
>          cannot be made whole (or treated as whole) without
>          you providing a run input file.
>
> Can someone say , why this warning msg is coming, and how should i need to
> avoid this. what measure should i need to take ?
>
>
>
>
> Thank you.
> --
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