AMBER Archive (2004)

Subject: Re: AMBER: Removal of rotation: Flying ice cube

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue May 18 2004 - 19:39:59 CDT

I'm not sure I understand what you are describing.
1) why not use positional restraints (ntr=1) instead of the high masses?
2) is your system solvated, periodic, GB solvent, etc ?
3) NSCM removes rotation and translatino of the entire system,
   but you say that your protein is not moving so NCSM will not
   help here. is the flexible part that is rotating only part of the system?
   if so, it sounds like you might have poor partitioning of energy between
   the high mass part and the flexible part. maybe try a different coupling
   scheme or maybe this is a result of your high masses. In any case,
   NSCM would probably not help (even if it worked, which for
   AMBER6 may not be working depending on your answert to question 2.
carlos

----- Original Message -----
From: "koby levy" <klevy_at_physics.ucsd.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, May 18, 2004 8:23 PM
Subject: AMBER: Removal of rotation: Flying ice cube

> Dear Amber users,
>
> I am simulating a system (using sander classic, Amber6) where part of the
> system is fixed (by setting very large mass for these atoms). I chose this
> way to freeze atoms (instead of ibelly) to be able to remove rotational
> motion. However, I notice that in most of the trajectories my system is
> trapped and the flexible region freely rotates while the protein is almost
> frozen. This is probably what was observed previously for DNA simulations
> (using Amber) as "The flying ice cube".
> In these simulations I apply the removal of rotation and translation
> by the NSCM. Does the NSCM work? Is a special treatment required to get
> rid of the rotation motion in such cases?
>
> thank you in advance for any suggestion,
> Koby Levy
>
>
>
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