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

From: David A Case <>
Date: Tue, 21 Jun 2011 13:54:25 -0400

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.]


AMBER mailing list
Received on Tue Jun 21 2011 - 11:00:03 PDT
Custom Search