Just out of curiosity, why can't you remove the waters? Do you want to
visualize water movement as well? In that case you could potentially
just remove the water hydrogens, which will still give you an idea of
how the water is moving while reducing the trajectory size.
-Dan
On Wed, Jan 9, 2019 at 8:17 AM Chetna Tyagi <cheta231.gmail.com> wrote:
>
> Hello,
>
> Thanks for the tip!
> I can't remove waters from this one but I will surely try the second
> suggestion...
>
> Thanks again!
>
> Chetna
>
> On Wed, Jan 9, 2019 at 1:42 PM Qinghua Liao <scorpio.liao.gmail.com> wrote:
>
> > Hello,
> >
> > Before you load your trajectories, you can remove waters and ions from
> > the trajectories,
> > or you don't need to load every frame, but load every XXX (for example,
> > 10) frames.
> >
> >
> > All the best,
> > Qinghua
> >
> > On 1/9/19 1:22 PM, Chetna Tyagi wrote:
> > > Dear all,
> > >
> > > This is not specifically an AMBER question but I would like to ask how
> > can
> > > we visualize large trajectories?
> > >
> > > I carried out three separate accelerated MD runs of 500 ns each. I want
> > to
> > > see how my peptide eventually interacts with the lipid bilayer.
> > > When I load it in VMD for visualization, the program just stops with an
> > > error like "Can't load any more frames".
> > >
> > > Is it a problem with VMD or that my computer's memory (16 GB) is
> > > insufficient? I could not find similar errors on VMD help forums.
> > >
> > > What are some other software or tools to visualize this? How did you
> > solve
> > > this problem?
> > > Thank you for any suggestions..
> >
> >
>
> --
> Best wishes
> Chetna
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Received on Wed Jan 09 2019 - 08:30:03 PST
