AMBER Archive (2006)

Subject: Re: AMBER: Unstable RMS trajectory

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Oct 17 2006 - 11:10:52 CDT

I think it is always a good idea to visually inspect the
trajectories and not to just trust rmsd values or other
numerical measures since there could always be a problem
in your analysis scripts.

Dave, Sonya wrote:

> Hi,
>
> I am minimizing a protein in water, using explicit solvent. I'm
> following the input files of the tutorial 1, part 3/4. Except, i am
> applying it to a protein.
>
> The vacuum minimization works fine, in that RMS stabilizes and EP tot
> decreases and stabilizes. However, for the water explicit
> minimizations, the RMS shoots off to high values, in a smooth
> continually increasing fashion. I am using the result of vacuum
> simulation PDB as the input for all my water simulations (i am first
> fixing the protein, the removing restraints, per the tutorial).
>
> I am plotting potential energy and RMS during the simulation. The PE
> initially spiked up, but now it's is decreasing and stabilizing (at a
> highly negative value). The RMS, however, continues to rise.
>
> Does this always mean there is something wrong with my simulation? Or
> do I have to make movies of the files to be sure? If it means
> something is wrong, how do i decide what to change to make it right?
>
> Thank you,
> Sonya Dave'

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu