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
> > > > >
> > > >
> > -----------------------------------------------------------------------
> > > > > The AMBER Mail Reflector
> > > > > To post, send mail to amber.scripps.edu
> > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > > > >
> > > >
> > >
> > -----------------------------------------------------------------------
> > > The AMBER Mail Reflector
> > > To post, send mail to amber.scripps.edu
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> >
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Jul 29 2007 - 06:07:37 PDT
