AMBER Archive (2006)

Subject: Re: AMBER: Unstable RMS trajectory

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Oct 17 2006 - 11:33:40 CDT

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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