Dear Carlos,
Thank you, your answer helped.
Regards,
Kailee
On 7/12/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> I see- if you are looking to see if gas *enters* the protein then you do
> want to use imaging. otherwise some that diffuse into a protein
> in a neighboring cell will not be shown when you view the protein in
> the main cell.
> whether you image or not really does depend on what you are trying
> to calculate, since all of the images exist in the calculation but
> only a single one is shown in the trajectory. you image if you want to
> see what is going on in the main cell, and you don't image if you want
> to track where the molecules move to (how far they diffuse during the
> simulation).
> hope that helps
>
> On 7/12/07, Kailee <kaileeamber.googlemail.com> wrote:
> > 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 - 06:07:25 PDT
