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
>
>
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Received on Thu Sep 01 2011 - 11:30:02 PDT
