[gmx-users] Protocol for Gromacs analysis

[anu chandra]

Thanks for the valuable replies.

@Tsjerk, I just wonder whether such jumps will happen when simulating
proteins in membranes.


Thanks once again

Anu


On Wed, Mar 2, 2016 at 10:32 PM, João Henriques <
joao.henriques.32353 at gmail.com> wrote:

> 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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