AMBER Archive (2007)

Subject: Re: AMBER: about wrap the trajectory

From: Rachel (comeonsos_at_googlemail.com)
Date: Fri Jul 27 2007 - 09:08:23 CDT

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_at_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_at_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_at_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_at_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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