[gmx-users] (no subject)

tasneem kausar tasneemkausar12 at gmail.com
Sat Nov 19 20:38:08 CET 2016

Dear Kingsley

You are directly calculating the rms after combining the xtc file. It is
clear from the warning that you did not apply perodic boundary condition on
you trajectory.

Try trjconv -f combined.xtc -s refrence.tpr -o combined_pbc.xtc -pbc whole
-center command after trjcat. After trjconv calculate RMS.

On Sat, Nov 19, 2016 at 11:06 AM, 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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