On Thu, Sep 1, 2011 at 2:40 PM, Keith Yarem <chemogan.yahoo.com> wrote:
> Is it necessary to keep using the modified (single molecule DNA) prmtop for
> subsequent simulations, or is that prmtop really only needed during the
> re-imaging procedure?
>
> I ran a quick test, and it looks like either prmtop will work for the
> simulation (the behavior of the DNA molecule appears to be the same).
>
The next version of AmberTools will probably contain a prmtop editor that
will enable this exact behavior automatically (it will take care of
adjusting the various pointers for you). However, this approach is *not*
strictly necessary for either imaging or for the simulation unless, as InSuk
said, you apply restraints between the different DNA strands (then it's
needed for the simulation, but not for imaging). If you are imaging, the
way you image everything together is to do one strand at a time. That is:
trajin trajectory.mdcrd
trajout centered.mdcrd
center :1-50 mass origin
image origin center familiar
center :1-100 mass origin
image origin center familiar
This is assuming each strand is 50 nucleobases. What this will do is center
the first strand, image everything back to it (which should move the second
strand back into the periodic box). The second "center" command will then
center the DNA duplex in the box, after which everything is imaged around
that.
HTH,
Jason
>
>
> ________________________________
> From: Keith Yarem <chemogan.yahoo.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Thursday, September 1, 2011 2:23 PM
> Subject: Re: [AMBER] Non-periodic behavior of NMR restraints upon restart
> in a periodic system
>
>
> This thread no longer has much to do with NMR restraints... It's all about
> re-imaging before restarting an MD run.
>
>
> Looks like I have to re-image my truncated octahedral system (9-mer DNA
> plus ions in TIP3) in this way:
>
> trajin ucstdb-1.mdcrd 3000 3000 1
> trajout new.ucstdb.rstrt restart
> image origin center familiar
>
> I did have to modify the .prmtop that I used for re-imaging so the DNA
> strands would be treated as a single molecule. I did this in the
> ATOMS_PER_MOLECULE section by combining the 2 entries for the 2 DNA strands
> and shifting the entries for ions and water as needed.
>
> Everything seems to be working well, but I have a couple of lingering
> questions:
>
>
> What about the ions proximal to the DNA? Am I losing their proper
> arrangement upon re-imaging my system, or does the re-imaging with ptraj
> maintain their positions w.r.t. the DNA correctly?
>
> Thanks so much!
>
> Keith
>
>
>
> ________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Tuesday, June 21, 2011 1:59 PM
> Subject: Re: [AMBER] Non-periodic behavior of NMR restraints upon restart
> in a periodic system
>
> my solution has been to modify the prmtop to put solute all in 1
> "molecule" for imaging. it's not trivial unless you know the prmtop
> format. it could probably be automated or made an option to leap if
> people felt it was a better solution. maybe Dave is right though that
> we should just not wrap until postprocessing.
>
>
> On Tue, Jun 21, 2011 at 1:54 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
> > On Tue, Jun 21, 2011, Keith Yarem wrote:
> >>
> >> When the two complementary DNA strands are imaged at opposite sides of
> >> the octahedral simulation cell at the time when the final restart file
> >> is written, the next simulation which uses those restart coordinates
> >> as a
> starting point fails to properly address the periodicity of the
> >> restraints on the terminal base pairs of separated strands.
> >>
> >> I'm using iwrap=1
> >
> > I don't think you can do that. The wrapping facility inside sander is
> very
> > primitive, and DNA strand separation is one bad thing that can happen.
> >
> > If the problem occurs only at the restart, you can use ptraj to correctly
> > image the system, save the coordinates in restart format, then paste back
> in
> > the velocities from the original restart file. This is a pain, but not
> hard
> > once you get the hang of it.
> >
> > [Posted as a long-time opponent of iwrap=1, so take with a grain of salt.
> > Perhaps others on the list have some better ideas.]
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 01 2011 - 13:00:02 PDT
