[gmx-users] Extract frames from Trajectory

[Harsha Ravishankar]

Hi Justin & Fernando,

Thanks for the replies. I think I might have not explained my issue
properly: so I have a 100 ns trajectory of a protein & lipids system. I
would like to extract frames every 1 ns of the protein and whatever lipids
might be within 0.2 nm within it.

The way I proceeded was as follows,

First, I made an index file containing the residues of the transmembrane
domain named residues.ndx,

Next i made use of gmx select to identify the lipid molecules which are 0.2
nm away from them in the trajectory using,

gmx select -f Traj.trr  -s topol.tpr -select 'resname POPC and within 0.2
of group 30' -n residues.ndx  -on Lipids.ndx,

Then I manually added the contents of Lipids.ndx to Protein.ndx, which
contains just the protein and renamed it as ProteinLipids.ndx

Next, I write out the frames using,

gmx trjconv  -f Traj.trr -s topol.tpr -o proteinlipid.pdb -split 1000 -dt
1000 -n ProteinLipids.ndx -pbc whole,

but I find that I am unable to.

I would be grateful for any suggestions on what to do,

cheers

Harsha

On Tue, Nov 27, 2018 at 4:41 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/27/18 10:24 AM, Fernando Nunes wrote:
> > Try use -dump option and put exact time of the frame you want.
>
> The trjconv -dump option requires manual selection of which frames to
> write, which could be quite cumbersome here.
>
> An alternate approach is to generate a time series with some values that
> indicate that the criterion is satisfied, either a boolean operator (1
> or 0) that indicates the lipid is within range, or use a minimum
> distance criterion to indicate whether a lipid is close to the protein.
> Then, one can use trjconv -drop to read that .xvg file and
> -dropover/-dropunder to automatically select the frames of interest.
>
> -Justin
>
> > Harsha Ravishankar <hara0050 at gapps.umu.se> escreveu no dia terça,
> > 27/11/2018 à(s) 15:16:
> >
> >> Hi,
> >>
> >> I need to extract frames from a 100 ns membrane protein simulation
> >> trajectory which contains the protein molecule and lipid molecules which
> >> are at a distance of 0.2 nm from its transmembrane domain.
> >>
> >> First, I made an index file containing the residues of the transmembrane
> >> domain named residues.ndx,
> >>
> >> Then i made use of gmx select to identify the lipid molecules which are
> 0.2
> >> nm away from them in the trajectory,
> >>
> >> gmx select -f Traj.trr  -s topol.tpr -select 'resname POPC and within
> 0.2
> >> of group 30' -n residues.ndx  -on Lipids.ndx,
> >>
> >> Here I get an index file containing indices of individual atoms, which I
> >> would like to use to extract frames of the protein + lipid molecules
> from
> >> the simulation trajectory, but i am not sure how to.
> >>
> >> Any help would be appreciated,
> >>
> >> Thanks
> >>
> >> Harsha
> >>
> >>
> >>
> >> --
> >> Harsha Ravishankar
> >> Doctoral Candidate
> >> Department of Chemistry
> >> Umeå University, Umeå, Sweden
> >> --
> >> Gromacs Users mailing list
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-- 
Harsha Ravishankar
Doctoral Candidate
Department of Chemistry
Umeå University, Umeå, Sweden