[gmx-users] Protocol for Gromacs analysis

[anu chandra]

Hi Tsjerk,

Thanks for the reply. As the description of gmx trjconv says, with -pbc
nojump, I do observed that the molecules (water and ions in case of
membrane simulation) diffused out of the box, as expected when one remove
the PBC. I just wonder whether this diffusion can affect any computing
properties of the membrane-protein system.

Many thanks
Anu

On Wed, Mar 2, 2016 at 7:55 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> > > > --
> > > > Gromacs Users mailing list
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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