AMBER Archive (2007)

Subject: Re: AMBER: about wrap the trajectory

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Jul 27 2007 - 11:10:49 CDT

yes that should work, check Tom Chaetham's posts for the exact syntax.

On 7/27/07, Rachel <comeonsos_at_googlemail.com> wrote:
> Dear Carlos,
>
> So as you mentioned in your last email, if I want to see all the water
> surround my solute, I should image center on the solute, does it mean I can
> get all the atoms in the system imaged back to the primary box if I centerd
> on the solute (including the protein, the gas molecules, the water)?
>
>
> regards,
> Rachel
>
>
>
> On 7/27/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> > 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_at_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_at_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_at_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_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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