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

[Bhupendra Dandekar]

Dear Rebeta

Did you visualise your trajectory? If not then kindly first do that.
If the protein in your CG simulation is fluctuating a lot then the rmsd of
3.5 can make sense.

Also, prepare a separate index for protein BB(backbone) bead only and use
it in rmsd fitting as well as rmsd calculation. There might be large
fluctuations in the sidechains compared to protein backbone which is giving
the resulting higher value of rmsd than expected.

Best wishes.
Bhupendra


On Wed, Jan 15, 2020 at 4:06 AM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> Hi,
>
> I am new user of GROMACS. I have run coarse-grained umbrella sampling
> simulation in GROMACS. I had prepared the system in CHARMM-GUI. After
> running the simulation, now I want to calculate the RMSD of the protein. I
> have used the following command to remove pbc effect first-
> gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
> -n index-all.ndx
>
> And then used the following command to calculate the RMSD-
>
> gmx rms -s step6.0_minimization.tpr -f 0A-2-pbc.xtc -fit rot+trans  -o
> rmsd-2 -pbc
>
> But after running the command, it asks to select group of least square fit,
> I choose protein and the RMSD value is too high around 3.5 nm. Can you
> please help me how I can calculate RMSD for coarse grained protein?
>
> Thanks.
>
> Rabeta Yeasmin
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