[gmx-users] how to calculate average structure

[mmousivand93]

Dear Dr. Subhomoi  

Hi,Thanks a lot for your answering. I use the gmx cluster command  as
follow 

"gmx-mpi cluster -f md300.trr -s md300.tpr -n index.ndx -cutoff 0.1 -cl
cluster.pdb" , then I got a pdb file with different models of my aptamer
without ligand, I need to check different interaction between aptamer
and ligand during simulation time.It would be pleasure if you have any
suggestion. 

Thanks a lot 

Maryam  

On 2019-10-05 08:43, Subhomoi Borkotoky wrote:

> 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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