[gmx-users] (no subject)
tasneemkausar12 at gmail.com
Sat Nov 19 20:38:08 CET 2016
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
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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