From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Jun 02 2011 - 11:11:28 CDT
There was a bug, fixed in NAMD 2.8, where if the coordinates and consref
used the same PDB file and a bincoordinates file was specified that the
coordinates from the bincoordinates file would over-write the shared
coordinates/consref data and thus shift the constraint positions. The
workaround for earlier versions is to use a different file name for
coordinates and consref (even a link will work) so NAMD can't tell that
it's actually the same file.
If you want "strong" constraints on the protein atoms you should use fixed
atoms rather than trying to approximate them with harmonic restraints.
On Thu, 2 Jun 2011, P.-L. Chau wrote:
> Could I ask for some help with more RMSD "jump" problems, please?
> I have been trying to equilibrate a protein. I used Ewald summation for
> the electrostatic interactions. The van der Waals interaction was handled
> without a switching function, but with long-range correction. I started
> off with strong harmonic constraints of the protein atoms, at 10K and with
> time-steps of 0.1fs each. I ran this system for 20ps, and the RMSD during
> this period fluctuated around 0.07AA. At the end of this run, I re-started
> the simulation and lengthened the time-step to 0.2fs, and I found that the
> RMSD jumped to over 2AA and stayed there. I then re-started from the same
> point, but used a time-step of 0.15fs, and I found that the RMSD jump
> Thinking that the van der Waals interaction could be the culprit, I re-did
> the simulations with a switching function (switchdist 10), but I saw the
> same effect. 0.2fs always caused an RMSD jump, and 0.15fs never did.
> It is well known that r.m.s. deviations fluctuate, but this was an abrupt
> increase in the value around which it fluctuated. I also checked that my
> boundary energy was finite, at 16991.6855.
> I could not think of any reason why lengthening the time-step would lead
> to such a dramatic change in protein structure. Could I ask if any other
> user has met with a similar problem? How do you deal with it?
> The graphs, analyses and NAMD files involved are quite large, since I am
> simulating a protein/membrane complex with >330000 atoms. So I am not
> including them here. If you would like to see them, please email me, and I
> shall put these files on a website and/or email them to you.
> Thank you very much!
> P-L Chau
> email: pc104_at_pasteur.fr
> Bioinformatique Structurale
> CNRS URA 2185
> Institut Pasteur
> 75724 Paris
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