AMBER Archive (2007)

Subject: Re: AMBER: about wrap the trajectory

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 27 2007 - 06:29:48 CDT

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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