[gmx-users] how to calculate average structure

[Subhomoi Borkotoky]

Hi

You can check the log file of the cluster output. An average time step will
be given representating the clusters in a tabular format. Note down the
time, accordingly dump it from the trajectory with trjconv. Use an index
file for the protein+ ligand.


Hope it helps.

On Mon, Oct 7, 2019, 11:24 AM mmousivand93 <mmousivand93 at ut.ac.ir> wrote:

> 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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