[gmx-users] Calculating C-alpha RMSD for coarse grained simulation

[Bhupendra Dandekar]

I will look into this and get back to you again. But meanwhile just try
using .tpr file instead of.gro file in your pbc correction step.

Thanks
Bhupendra

On Thu, Jan 16, 2020, 10:07 PM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi Bhupendra,
>
> Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
> very large compared to the RMSD of that protein in all-atom simulation
> which is mostly between 5-6A. I have checked the trajectory as you
> suggested, My system is a dimer protein inside a lipid bilayer and it looks
> like if I remove the pbc effect using the following command
> *gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
> -n index-all.ndx*
>
> the protein structure get stretched all the time  which causes the RMSD to
> be so high all-the time. If I use the original trajectory, the RMSD is
> usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
> wondering how can I remove pbc effect without stretching the protein and
> keeping the dimer as a whole.
>
> Thanks.
> Rabeta Yeasmin
>
>