From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jul 29 2016 - 10:55:51 CDT
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.
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
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