From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jul 29 2016 - 12:25:49 CDT
No I haven't. Is that igb=1 in AMBER?
I did some implicit solvent stuff in OpenMM, which supports equivalents of
igb=2,5 and 7. It runs quickly on GPUs.
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
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:36 CST