Your question is not quite clear to me but you probably need the modified
prmtop for your simulations if you apply restraints between two DNA starnds
and use iwrap=1. If you apply restraints between a DNA strand and an ion,
you'd better turn off iwrap (iwrap=0). And occasionally do 'image' using
ptraj before you restart in order to prevent solvent from drifting away out
of the maximum precision.
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).
>
>
>
> ________________________________
> 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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--
Best,
InSuk Joung
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Received on Thu Sep 01 2011 - 12:30:04 PDT
