AMBER Archive (2006)

Subject: RE: AMBER: Unstable RMS trajectory

From: Dave, Sonya (sonya.dave_at_vanderbilt.edu)
Date: Tue Oct 17 2006 - 12:17:59 CDT

It's RMSd. Sorry for being unclear.
In case i'm misunderstanding something, this is what I do to plot:

I make a text file cbs2on2_md2b.calcrms which contains

trajin cbs2on2b_md2b.mdcrd
rms first mass out cbs2on2b_md2b.rms time 0.1

and then at the command line, I type:
$AMBERHOME/exe/ptraj cbs2on2b_wat.prmtop < cbs2on2_md2b.calcrms
xmgr cbs2on2b_md2b.rms

Thank you for all the help.

Sonya
-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Gustavo Seabra
Sent: Tue 10/17/2006 11:56 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: Unstable RMS trajectory
 
I think that was my mistake here... I assumed RMSD, but she wouldn;t
be able to calculate RMSD without a trajectory, which the minimization
doesn't provide. So it must be the RMS energy, which comes from the
minimization output.

Sorry!

Gustavo.

On 10/17/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> good point- what RMS are we talking about, the
> energy gradient during minimization or a structure RMSD?
> if it's energy, then that doesn't say anything about the
> structure and one should investigate why the minimization
> is not working- perhaps due to overlap with water? checking
> to see which atom has the highest gradient can be helpful if
> combined with visual analysis of the region near that atom in
> the initial structure.
>
> Gustavo Seabra wrote:
>
> > Would you not expect the vacuum structure to be different than the
> > solvated one? Assuming it is not an error, I think we should expect
> > the RMSD to increase as you go from the vacuum to the solvated
> > structure.
> >
> > However, a movie would still be the best way to tell. The only problem
> > is that, as I understand, this is a minimization, right? How can she
> > generate a movie from the minimization? (I tried it before, but my
> > mdcrd files came up empty...)
> >
> > Gustavo.
> >
> > On 10/17/06, Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> >
> >> 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'
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