[gmx-users] how to calculate average structure

[Subhomoi Borkotoky]

Hi,

You can use "gmx cluster" to get an average structure based on RMSD. Just
use an appropriate cut-off.

Regards,

Subhomoi B.

On Sat, Oct 5, 2019, 10:01 AM mmousivand93 <mmousivand93 at ut.ac.ir> wrote:

> Dear all;
>
> I performed a molecular dynamic simulation(50ns) for a complex
> aptamer-ligand and I am going to analysis the interaction between
> aptamer and ligand during the simulation,then I will need the average
> structure.
>
> How can I calculate the average structure, is it correct to
> use the following command "GMX DCOVAR -F TRAJ.XTC -S TOPOL.TPR -B 801 -E
> 1000 -AV <OUT-PUT-FILENAME>.PDB" , when I used the command, I should
> select two group as "THE LEAST SQUARES" and "COVARIANCE ANALYSIS", which
> group must be selected,aptamer or system or ligand?
>
> Thanks a lot
> --
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