yes, it will be sensitive. you'll need to think about
what you want to measure and do the imaging to give you that
data. there's not one correct way to do it for all problems.
On 7/27/07, Rachel <comeonsos.googlemail.com> wrote:
> Dear Carlos,
>
> Thank you for your prompt reply. In my case, I want to see how many and
> which gas molecules at what time get into the protein and their pathways,
> positions etc., will all these be the same if I used different centers? I am
> wondering if by using different centers different atoms are imaged back to
> the primary box, then if I used wrong 'center', even I got the 'real'
> trajectories, some of my gas molecules for example may not be imaged back so
> when I analyze the results, it may cause some differences.
>
> Best regards,
>
> Rachel
>
>
> On 7/27/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> > all of the different centering options give the same trajectory
> > in the sense that all are correct representations of what goes on
> > in the simulation. Which you choose depends how how you want
> > to view or analyze the system. normally if you want to see all of
> > the water surround your solute you will center on the solute and
> > then image. with more than 1 solute molecule (such as a DNA
> > duplex) you need to do this in several steps.
> > all are "real" trajectories, they just differ in which parts of the
> > periodic system are moved into the central box.
> >
> > On 7/27/07, Rachel < comeonsos.googlemail.com> wrote:
> > > Dear Carlos,
> > >
> > > Thank you for your reply. I did some search for cheatham, ptraj and
> image,
> > > there are a lot of archives on using ptraj to image trajectories,
> however, I
> > > still not sure what will be the differences using different centers to
> image
> > > the trajectories. Here is what my system like and what I did:
> > >
> > > I am currently using AMBER8 to run md, and my system is a protein with
> some
> > > gas molecules diffusiong into the protein, and both the protein and gas
> > > molecules are solvated using truncated octahedral TIP3P water box. The
> iwrap
> > > was set to 0 during all the md, and I want to wrap the trajectories back
> to
> > > the primary box after md for analysis. And I used the following script
> in
> > > ptraj to image the trajectories:
> > > trajin md1_6th.mdcrd.gz
> > > trajin md2_6th.mdcrd.gz
> > > trajin md3_6th.mdcrd.gz
> > > trajin md4_6th.mdcrd.gz
> > > trajin md5_6th.mdcrd.gz
> > > trajout reimage_md1to5_6th.mdcrd.gz
> > > center
> > > image familiar
> > > go
> > >
> > > If using different 'center' in the script will change the trajecotries,
> then
> > > should I center on all the atoms, on protein, or on protein plus gas
> > > molecules, which will give the real trajectories of the system? and how
> > > about center on the mass? are there any other keywords in the script
> that
> > > may change the trajecotries to what they should be? thank you very much
> for
> > > your help.
> > >
> > > Kind regards,
> > > Rachel
> > >
> > >
> > > On 7/27/07, Carlos Simmerling < carlos.simmerling.gmail.com> wrote:
> > > >
> > > > yes it will. you should center on the protein.
> > > > Tom Cheatham might be able to comment on which
> > > > centering matches what sander is doing. there are also
> > > > lots of examples from him in the archives that you might
> > > > want to read. do a search for cheatham, ptraj and image.
> > > >
> > > > On 7/26/07, Rachel < comeonsos.googlemail.com > wrote:
> > > > > Dear Carlos,
> > > > >
> > > > > Thank you for your reply. I used VMD (which has some pbc wrap tools)
> to
> > > wrap
> > > > > the trajectory and as I compared it with that after I used ptraj,
> they
> > > are
> > > > > completely different, that's why I am wondering if I did something
> wrong
> > > or
> > > > > it's because of the box I used.
> > > > >
> > > > > I have another small question, I used ptraj to wrap the box as
> > > following:
> > > > >
> > > > > trajin md1_6th.mdcrd.gz
> > > > > trajin md2_6th.mdcrd.gz
> > > > > trajin md3_6th.mdcrd.gz
> > > > > trajin md4_6th.mdcrd.gz
> > > > > trajin md5_6th.mdcrd.gz
> > > > > trajout reimage_md1to5_6th.mdcrd.gz
> > > > > center
> > > > > image familiar
> > > > > go
> > > > >
> > > > > What I want to ask is will it change the trajectories if I used
> center
> > > for
> > > > > all the atoms, or if I used center for only the atoms in the
> protein,
> > > like:
> > > > > trajin md1_6th.mdcrd.gz
> > > > > trajin md2_6th.mdcrd.gz
> > > > > trajin md3_6th.mdcrd.gz
> > > > > trajin md4_6th.mdcrd.gz
> > > > > trajin md5_6th.mdcrd.gz
> > > > > trajout reimage_md1to5_6th.mdcrd.gz
> > > > > center : 1-5668
> > > > > image familiar
> > > > > go
> > > > >
> > > > > Thank you for your answer.
> > > > >
> > > > > Rachel
> > > > > On 7/26/07, Carlos Simmerling < carlos.simmerling.gmail.com > wrote:
> > > > > >
> > > > > > if you wrap in ptraj there's really no way to wrap to a
> rectangular
> > > > > > box- and if you did, some molecules may overlap. you should
> > > > > > wrap back to the same box used in the MD unless you really know
> > > > > > what you're doing (and can go through the extra steps you would
> need)
> > > > > >
> > > > > > On 7/26/07, Rachel <comeonsos.googlemail.com > wrote:
> > > > > > > Dear all,
> > > > > > >
> > > > > > > I solvated my protein with truncated octahedral water box, and
> the
> > > iwrap
> > > > > is
> > > > > > > set to 0, and I want to image the trajectory back to primary box
> for
> > > > > > > analysis, can I ask if I used a rectangular box rather than a
> > > truncated
> > > > > > > octahedral box to wrap the trajecotries, will that change the
> > > > > trajectories
> > > > > > > or the results would still be the same? thank you.
> > > > > > >
> > > > > > > Kind regards,
> > > > > > > Rachel
> > > > > >
> > > > >
> > >
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Received on Sun Jul 29 2007 - 06:07:37 PDT
