From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Fri Jul 29 2016 - 11:20:46 CDT
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/
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