[gmx-users] Protocol for Gromacs analysis

[João Henriques]

There is no way to combine steps 1 and 2. Either you remove the PBC of each
replicate and then concatenate them, or you concatenate first and then
remove the PBC. Either way yields the same results.

Just a friendly warning: Be very careful with how you perform the
statistics on concatenated (discontinuous) trajectories, specially when
estimating correlation-corrected errors.

/J

On Wed, Mar 2, 2016 at 5:33 PM, anu chandra <anu80125 at gmail.com> wrote:

> Dear Gromcas users,
>
> I am quite new to Gromacs and I have just completed 100 ns simulation of a
> membrane protein using Gromcas. Now, I would like to do some basic analysis
> like RMSD, RMSF, Hydrogen bonding etc with the 100 ns trajectories. Below,
> I just wrote down the steps I adapted to generate the necessary preparatory
> files for different analysis with Gromacs analysis tools. I will be
> grateful if the experts in the community can help me with the their
> suggestion, if I am doing anything wrong here.
>
> Step-1 : Concatenate all the trajectories, which I have run as 5 ns window
> each, and generate a single 100 ns trajectory.
>
> gmx trjcat -f 1md.trr 2md.trr 3md.trr 4md.trr 5md.trr 6md.trr 7md.trr
> 8md.trr 9md.trr 10md.trr -o 1_10md_concat.xtc
>
> Step-2: Remove the PBC
>
> gmx trjconv -f 1_10md_concat.xtc -o noPBC.xtc -s md.tpr -pbc mol -ur
> compact
>
>
> Step-3: Make the necessary index file if one want to do analysis with any
> specific group of atoms/molecule
>
> gmx make_ndx -f md.gro -o index.ndx
>
>
> Step-4: Do the analysis with different Gromcas analysis tools ( gmx rmsd,
> gmx cluster etc.) using the files from step-2 and step-3
>
>
> Am I doing any thing wrong here? Is there any fine tuning required in these
> steps? Is there a way to combine the steps 1 and 2?
>
>
> Many thanks in advance
>
> Anu
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