Dear Carlos,
Thank you for your reply.
I thought the physical meaning of the wrapped and unwrapped states should be
the same as well, however, as I looked at the results using VMD, the number
of gas molecules diffused into the protein at the same time is different
with wrap on and off. Here is how I did:
The system I am looking at is a protein (with 672 residues) with 200 gas
residues initially placed outside the protein, the whole system was solvated
with TIP3P water using octahedral box (having 10300 water residues), thus in
total there are 11172 residues.
During all the MD simulation (4 ns long), the iwrap was set to 0 as default.
And the wrapped trajectories were obtained using ptraj, here is the script I
used (named reimage.ptraj):
trajin md1.mdcrd.gz
trajout md1_reimage.mdcrd.gz
center :1-872
image familiar
go
$AMBERHOME/exe/ptraj model.prmtop < reimage.ptraj
Then I loaded unzipped md1.mdcrd and md1_reimage.mdcrd into VMD to look at
the results, for these two sets of results at the same time, the number of
gas molecules inside the protein are different which should not be the case?
is there any mistake in using the ptraj script that caused this difference?
Thank you all for your help.
Regards,
Kailee
On 7/12/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> they won't be inside the protein. when you use wrapping, when a molecule
> leaves the central unit cell it is removed and translated to where the
> periodic image of that molecule entered the unit cell. with wrapping off,
> you always track the same molecule even when it leaves the unit cell.
> both are the same physically, since it is a periodic system the periodic
> images of the molecules "exist" in the simulation. the only change is
> which
> images of the molecule are written to the file. all of them are present in
> the simulation.
>
> taking a look at some of the images of periodic systems might help, you
> can do
> a gogole search for "periodic boundary conditions" and click on images.
> for example, CCL has a good explanation:
> http://www.ccl.net/cca/documents/molecular-modeling/node9.html
>
>
> On 7/12/07, Kailee <kaileeamber.googlemail.com> wrote:
> > Hi, David,
> >
> > Thank you for your reply.
> >
> > Can anyone tell me more about the differences between the wrapped and
> > unwrapped states please? from my results, gas molecules that are outside
> the
> > protein if unwrapped may become inside the protein when the trajectory
> is
> > wrapped into the primary box, therefore the results could be obtained
> will
> > be totally different. I really want to know which states indicate the
> real
> > situation. Thank you.
> >
> > Best regards,
> > Kailee
> >
> >
> > On 7/12/07, David A. Case <case.scripps.edu> wrote:
> > > On Wed, Jul 11, 2007, Kailee wrote:
> > > >
> > > > As said in AMBER manual, set iwrap=1 can wrap the trajectory files
> into
> > the
> > > > primary box that can make structure more visually but can mess up
> > diffusion
> > > > and other calculations. I am looking at the gas molecule diffusing
> into
> > a
> > > > protein, and need to look at the gas diffusion pathways, what I want
> to
> > ask
> > > > is when I look at the diffusion pathways should I reimage the
> > trajectories
> > > > into the primary box or not? as after wrapped into the primary box,
> the
> > gas
> > > > trajectories are quite different from those before wrapping and
> become
> > > > incontinuous. I am now a bit confused, which (before or after wrap)
> > states
> > > > are the real situation that I need to do my analysis?
> > >
> > > Sounds to me like you want to use the un-wrapped (continuous)
> > trajectories.
> > > Your situation sounds like one where wrapping is not a good idea.
> > >
> > > ...good luck...dac
> > >
> > >
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Received on Sun Jul 15 2007 - 06:07:24 PDT
