From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jul 29 2016 - 14:24:21 CDT
I have never done a comparison against the AMBER results, but I've had good
comparison to experiment when doing things with OpenMM.
OpenMM runs extremely fast on GPUs with implicit solvent, comparable or
even slightly faster than AMBER in my experience, and certainly faster than
NAMD for these applications.
Yes, OpenMM does support the HCT model. If you download the source (
https://simtk.org/projects/openmm), it comes with documentation, and you
can see the implicit solvent models available on page 16 of the
OpenMMUsersGuide.pdf.
On Fri, Jul 29, 2016 at 2:18 PM, Thomas Evangelidis <tevang3_at_gmail.com>
wrote:
>
> > No I haven't. Is that igb=1 in AMBER?
>
> Yes.
>
> > I did some implicit solvent stuff in OpenMM, which supports equivalents
> of igb=2,5 and 7. It runs quickly on GPUs.
>
> But do you know if it supports igb=1? I can rank the ligands of a specific
> protein better with this model, and I am looking for a commercial free code
> to run on GPUs. Have you noticed the perfomance of OpenMM to be better on
> GPUs than NAMD? Could you reproduce with OpenMM the results you obtained
> with AMBER using the afore-mentioned GB models?
>
> > I think the AMBER and OpenMM SASA calculations are a bit more
> approximate than those in NAMD, but are in a form that transfers well to
> the GPU.
>
> >
> > On Fri, Jul 29, 2016 at 12:20 PM, Thomas Evangelidis <tevang3_at_gmail.com>
> wrote:
> >>
> >>
> >>
> >> On 29 July 2016 at 17:55, Aron Broom <broomsday_at_gmail.com> wrote:
> >>>
> >>> I recall having this same question some years ago, and as I recall the
> answer was yes, you do need "sasa on".
> >>>
> >>> The method for calculating SASA that is used by NAMD (at least as of
> version 2.8) isn't exactly identical to that used by AMBER, so expect some
> difference in that energy term if you are comparing the two.
> >>>
> >>> I don't know if it is still the case, but as least in NAMD 2.8, the
> sasa calculation was very performance draining, at least when trying to
> accelerate the simulation using GPUs (I think the sasa calculations had not
> been ported to the GPU). Maybe that is no longer the case.
> >>>
> >>
> >>
> >> Thanks, they still slow down the performance a lot on GPUs!
> >> Have you ever tried to use the GB-HCT model in NAMD?
> >>
> >>
> >>
> >>>
> >>>
> >>> On Fri, Jul 29, 2016 at 11:26 AM, Thomas Evangelidis <
> tevang3_at_gmail.com> wrote:
> >>>>
> >>>> Greetings,
> >>>>
> >>>> I know NAMD supports the GB-OBC models I and II for implicit solvent
> simulations [1], which correspond to AMBER parameter igb=2 and igb=5
> values, respectively. One simply has to change GBISDelta, GBISBeta, and
> GBISGamma values to switch between these two models. Is it necessary to
> activate surface tension (NAMD parameters "sasa on" and "surfaceTension
> 0.0072", as in AMBER)?
> >>>>
> >>>> Also, is it possible to use with NAMD the older
> >>>>
> >>>> GB-HCT model [2], which corresponds to AMBER parameter igb=1?
> >>>>
> >>>> thanks in advance,
> >>>> Thomas
> >>>>
> >>>>
> >>>> [1] Onufriev, A.; Bashford, D.; Case, D. Exploring protein native
> states and large-scale conformational changes with a modified generalized
> Born model. Proteins, 2004, 55, 383–394.
> >>>> [2] Tsui, V.; Case, D. Molecular dynamics simulations of nucleic
> acids using a generalized Born solvation model. J. Am. Chem. Soc., 2000,
> 122, 2489–2498.
> >>>>
> >>>>
> >>
> >> --
> >>
> >> ======================================================================
> >>
> >> Thomas Evangelidis
> >>
> >> Research Specialist
> >>
> >> CEITEC - Central European Institute of Technology
> >> Masaryk University
> >> Kamenice 5/A35/1S081,
> >> 62500 Brno, Czech Republic
> >>
> >> email: tevang_at_pharm.uoa.gr
> >>
> >> tevang3_at_gmail.com
> >>
> >>
> >> website: https://sites.google.com/site/thomasevangelidishomepage/
> >>
> >>
> >
> >
> >
> > --
> > Aron Broom M.Sc
> > PhD Student
> > Department of Chemistry
> > University of Waterloo
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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