Dear Jiayun,
I've just had a paper accepted by Molecular Simulations comparing GBSA
and explicit solvent unfolding simulations in AMBER. This was undertaken
on the model system Barnase and compared simulations at 500K using
explicit solvent with PME with simulations at 400K, 450K and 500K using
GBSA with an 18Angstrom cut-off. This cutoff value was chosen by using a
range of cutoffs from 14 - 24 Angstrom and running short simulations
from the same starting conditions to look for differences in the
calculated Electrostatic energy. 18Ang seemed to be the point where the
change in Electrostatic energy levelled off, although there was still
larger energies at 20 - 24Angstrom, the time taken was much longer. You
should undertake similar short runs with different cut-offs yourself as
different proteins will behave differently.
I also found that the highest temperature of 500K unfolded Barnase
extremely rapidly with GBSA, whilst 400K only got to the first
intermediate on the pathway. You might like to try lower temperatures to
study the unfolding pathway in more detail. The 500K explicit solvent
method took more nanoseconds to unfold than the 450K GBSA simulations.
I can't help with the dimer problem, other than to suggest that you
might try adding a weak restraining force between the molecules.
Andy Purkiss
On Thu, 2004-01-29 at 10:47, Jiayun Pang wrote:
> Hi, thanks to all the answers.
>
> Carlos, you mentioned it's not a good idea to use cutoff in GB. I read the
> GB tutorial in the amber website. Ideally, one should use no cut-off , but
> as I found in my case, it is too computationally expensive. In the previous
> discussion in the amber reflector, it is said larger values, such as 15 to
> 24 A could be considered in GB. I assume, as it is said in the tutorial ,
> it is the trade between the speed and accuracy of the simulations. Do you
> have any suggestions?
>
> I am using Amber7 with the mpi run before. As you suggested, I have a
> shorter run with single processor. The dimer run is 4.2 times longer the
> monomer run. It seems the time allocation among GB parameters are different.
>
> The following is the detailed analysis at the end of the output file for the
> Dimer run.
> ----------------------------------------------------------------------------
> ----
> 5. TIMINGS
> ----------------------------------------------------------------------------
> ----
>
> | Calc gb radii 683.05 (19.52% of Gen B)
> | Calc gb diag 2211.56 (63.20% of Gen B)
> | Calc gb off-diag 465.40 (13.30% of Gen B)
> | Surface area energy 139.50 ( 3.99% of Gen B)
> | Gen Born time 3499.51 (100.0% of Nonbo)
> | Nonbond force 3499.51 (99.40% of Force)
> | Bond energy 0.39 ( 0.01% of Force)
> | Angle energy 4.57 ( 0.13% of Force)
> | Dihedral energy 16.30 ( 0.46% of Force)
> | Force time 3520.77 (99.86% of Runmd)
> | Shake time 2.74 ( 0.08% of Runmd)
> | Verlet update time 2.17 ( 0.06% of Runmd)
> | Runmd Time 3525.68 (100.0% of Total)
> | Total time 3387.34 (100.0% of ALL )
>
> | Highest rstack allocated: 58894
> | Highest istack allocated: 21416
>
> | Setup wallclock 1 seconds
> | Nonsetup wallclock 3387 seconds
>
>
> The Monomer output is,
> ----------------------------------------------------------------------------
> ----
> 5. TIMINGS
> ----------------------------------------------------------------------------
> ----
>
> | Calc gb radii 274.64 (31.91% of Gen B)
> | Calc gb diag 347.72 (40.40% of Gen B)
> | Calc gb off-diag 171.48 (19.92% of Gen B)
> | Surface area energy 66.88 ( 7.77% of Gen B)
> | Gen Born time 860.72 (100.0% of Nonbo)
> | Nonbond force 860.72 (98.87% of Force)
> | Bond energy 0.14 ( 0.02% of Force)
> | Angle energy 1.98 ( 0.23% of Force)
> | Dihedral energy 7.68 ( 0.88% of Force)
> | Force time 870.52 (99.83% of Runmd)
> | Shake time 0.71 ( 0.08% of Runmd)
> | Verlet update time 0.78 ( 0.09% of Runmd)
> | Runmd Time 872.01 (100.0% of Total)
> | Total time 805.65 (100.0% of ALL )
>
> | Highest rstack allocated: 29447
> | Highest istack allocated: 10708
>
> | Setup wallclock 0 seconds
> | Nonsetup wallclock 805 seconds
>
>
> ----- Original Message -----
> From: "Carlos Simmerling" <carlos.csb.sunysb.edu>
> To: <amber.scripps.edu>
> Sent: Wednesday, January 28, 2004 6:26 PM
> Subject: Re: AMBER: A few questions in the protein unfolding simulations
> using GB model
>
>
> > I would suggest taking a closer look at the detailed timings provided at
> the
> > end of the sander output, and running single cpu so as not to confuse
> > the issue even more with different scaling efficiencies for the systems.
> >
> > GB certainly doesn't scale linearly, but you're also using a cutoff
> (perhaps
> > not a good idea) so it's not be N^2 as someone suggested.
> > also GB doesn't use a pairlist, so it isn't pairlist generation as Bill
> > suggested.
> >
> > run shorter benchmarks to test this, you should get reliable timings
> > with a 15 minute or so run, no need to run for days.
> >
> > which amber version is this?
> >
> > carlos
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
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> >
> >
> >
>
>
>
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--
"The clever cat eats cheese and breathes down rat holes with baited
breath. " W. C. Fields
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| Andy Purkiss, School of Crystallography, Birkbeck College, London |
| E-mail a.purkiss.mail.cryst.bbk.ac.uk |
| Phone 020 7631 6869 (Work) or 020 7237 1165 (Home) |
| Mobile: 07763 490 360 |
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Received on Fri Jan 30 2004 - 18:56:04 PST
