Dear Dr. Roe,
Yes, I assume this peptide will disrupt the membrane and and make way for
an ion channel sort of thing (I am not sure what I am looking for as it's a
new peptide).
I don't how long it would take in simulation time.
Thanks for the suggestion, I will definitely try it.
-Chetna
On Wed, Jan 9, 2019 at 5:14 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
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>
--
Best wishes
Chetna
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Received on Wed Jan 09 2019 - 08:30:04 PST
