AMBER Archive (2007)

Subject: Re: AMBER: rst overflow for implicit REMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jun 26 2007 - 10:35:47 CDT

with a dimer I am not sure if that is correct if the problem is that the
CM of the system (the dimer) is still at the origin.
the monomers may drift far apart. in essence, what you are simulating
is two monomers at infinite dilution. you probably should set a restraint
to keep the centers of mass from getting too far apart, or write some code
to keep the monomers inside a virtual box.

On 6/26/07, David A. Case <case_at_scripps.edu> wrote:
>
> On Tue, Jun 26, 2007, In Hee Park wrote:
> >
> > Although setting "iwrap=1" is recommended to keep the coordinate output
> > from overflowing the trajectory file format, this option can be used PME
> > run only. Now, it just shifting to explicit(or hybrid)-REMD the only
> > possible way to make my dimer REMD possible? Is there no way to resolve
> > the overflow problem under GB?
> >
>
> I think the nscm option can be used to do what you want for GB runs.
>
> ...dac
>
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