Re: [AMBER] Non-periodic behavior of NMR restraints upon restart in a periodic system

From: Carlos Simmerling <>
Date: Tue, 21 Jun 2011 13:59:02 -0400

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 <> 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 Tue Jun 21 2011 - 11:00:04 PDT
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