AMBER Archive (2006)

Subject: Re: AMBER: Unstable RMS trajectory

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Oct 17 2006 - 12:41:43 CDT

Thanks, I feel better now :-)

I believe that, if you do not provide a mask, your script will
calculate the RMSd for all atoms, and that would include the waters as
well. But since the waters will naturally diffuse, your RMSd must
diverge.

Maybe if you change the line in your script to list a mask in the end:

rms first mass out cbs2on2b_md2b.rms time 0.1 @CA,C,N

you can get better results. I'm not really sure how important the
'mass' keyword there is.

Gustavo.

On 10/17/06, Dave, Sonya <sonya.dave_at_vanderbilt.edu> wrote:
>
>
>
> 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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> 

-- 
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Gustavo Seabra                                    Postdoctoral Associate
Quantum Theory Project                             University of Florida
Registered Linux user number 381680
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