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

[Rabeta Yeasmin]

Hi,

I have solved the issue. I had problem in pbc correction step. It is good
to follow some steps in order to get a good result. What I have used is
-First made the molecules as whole to remove stretching in the structures
(protein, membrane) due to pbc effect.
*gmx trjconv -s step6.0_minimization.tpr -f 0A-1.xtc -o 0A-1-pbc-whole.xtc
-pbc whole -n index-all.ndx*

But my protein is a dimer, this command made the two monomer separated.
That's why I had to cluster the two monomer after the above command.
*gmx trjconv -s step6.0_minimization.tpr -f 0A-1-pbc-whole.xtc -o
0A-1-pbc-whole-cluster.xtc -pbc cluster -n index-all-new.ndx*

I had calculated the RMSD after this, it looks reasonable now.
Thanks for suggesting to check the trajectory.

Rabeta Yeasmin

On Thu, Jan 16, 2020 at 10:46 AM Bhupendra Dandekar <
bhupendra.dandekar001 at gmail.com> wrote:

> 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
>>
>>