Hi,
The most important output of a simulation is the trajectory, generally in
.nc or .mdcrd format when using Amber.
This trajectory, in simple words, consists of "snapshots" of your
simulation taken after every specific time-step, for example, after every 2
ps, a snapshot will be saved
and the coordinates will be saved. Each such snapshot is referred to as
"frames".
So, my 500 ns long simulation is made of 250,000 frames as the time step is
2 ps.
1 nano second = 1000 pico second
500 ns = 500,000 ps which shall be the frame number if the time step is
only 1 ps....
Hope it helps..
this is how I understood it the first time...
On Wed, Jan 9, 2019 at 1:59 PM Mehreen Ghufran <mehreen.awkum.edu.pk> wrote:
> hi
> could anyone explain me about "Frames" in md simulation?what is meant by
> Frames in md simulation.
> Best regards
>
> On Wed, Jan 9, 2019 at 5:46 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..
> >
> >
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> >
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>
--
Best wishes
Chetna
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Received on Wed Jan 09 2019 - 05:30:02 PST
