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

[Bhupendra Dandekar]

You welcome. Also there is detail information on the pbc correction on
gromacs page, kindly see that.

Bhupendra

On Fri, Jan 17, 2020, 4:02 AM Rabeta Yeasmin <rabetayeasmin at gmail.com>
wrote:

> 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
>>>
>>>