it might be useful to run minimization and ntpr=-1, and look at the atom
with the highest forces (GMAX) in the output. Visually inspect the region
around that atom.
On Tue, Sep 27, 2011 at 12:13 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Voytek,
>
> > Thank you for the thorough review of my GB protocol for a large
> > RNA structure. I implemented all the indicated changes (most
> > importantly
> > moving to the Langevin thermostat), ran the equilibration for a total
> > of 1ns and
> > followed with MD. Unfortunately, the final results are a slow-motion
> > version
> > of the earlier structural failures, with the base pairs involving the
> > 5' and 3'
> > nucleotides, in the middle of otherwise robust, all-paired helices (
> > can be
> > viewed as two stacked helices) opening first, followed by the failure
> > of the
> > stacking (bending), rotations of the two halves around the connecting
> > backbone and slow flattening of the helices. If these are indicators
> > of known
> > problems (with prep or GB itself), I would appreciate more
>
> I am still hoping that someone familiar with running nucleic acid
> simulations with GB will chip in here. From what you describe though it
> looks like something is more fundamentally wrong with the simulation than
> just issues with how GB describes nucleic acids. I am assuming you see
> these
> changes on a fairly short <10ns timescale?
>
> It would be useful to see your output for the first step to see if any of
> the energies look off the scale. Beyond that I would check the GB radii in
> the prmtop file - perhaps there is something in there with a strange radii,
> zero perhaps? - Although I would expect this to show up in the GB energy in
> the output. The other options might be an atom with a very high charge or
> some other strange parameter.
>
> I also would not rule out any steric clashes going on - so you might want
> to
> check for close contacts.
>
> I would also try just turning off the restraints entirely at the beginning
> and see if the behavior is still there. It could be something weird going
> on
> with the restraints.
>
> Also, did you run the test cases for AMBER? - Just to make sure it isn't
> something wrong (a compiler bug for example) in the compilation of the GB
> code.
>
> > information on it.
> > No such issues occur in the explicit solvent approach.
> >
> > Dr. Walker commented that "GB will be terrible for highly polar systems
> > such
> > as DNA / RNA," and my experience seems to second that. On the other
> > hand,
> > GB protocol tutorial I read uses a small DNA fragment. Again, any
> > enlightening
> > comments would be appreciated (say, good for small nucleic acid
> > structures,
> > based on crystallography data, bad in other cases.)
>
> You are referring to the first tutorial here which is Tutorial B1. The
> purpose of this tutorial is to get brand new users up to speed on running
> AMBER. It is not designed to make any comment on the perfect input settings
> to use or the correct for field description for a simulation. DNA was used
> here since it is easy to build with the tools in AMBER so avoids the
> complexity of dealing with pdb files from the beginning. It is also good
> for
> demonstrating the issues with gas phase simulations. Beyond that GB is used
> just to highlight that one can run implicit solvent simulations as well as
> explicit solvent simulations. It is not designed to suggest that GB is
> optimum here for the arbitrary choice of solute molecule.
>
> > Also, with a cutoff of 999, the GB execution speed (even with PMEMD)
> > for
> > my 264nt RNA structure appears to be comparable to the explicit solvent
> > MD runs (on the order of 1ns of simulation time per day on a 24 core
> > cluster),
> > as suggested by Dr. Walker.
>
> Oh you are good then. The performance can be very hardware specific but one
> thing you may find is that the GB run will scale further than the implicit
> solvent case.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
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Received on Tue Sep 27 2011 - 10:00:03 PDT
