[gmx-users] Protocol for Gromacs analysis

[Tsjerk Wassenaar]

Hi Anu,

With oligomers, sure.

Cheers,

Tsjerk

On Wed, Mar 2, 2016 at 8:39 PM, anu chandra <anu80125 at gmail.com> wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.