Re: Generalized Born solvation models supported by NAMD

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Aug 02 2016 - 17:54:08 CDT

Hi Aaron,

Thanks for your input.

Chitrak.

On Tue, Aug 2, 2016 at 10:41 AM, Aron Broom <broomsday_at_gmail.com> wrote:

> Hi Chitrak,
>
> I think there may be some dependence of the implicit solvent parameters on
> the forcefield. I've always used AMBER forcefields, so I can't say for
> sure.
>
> I suspect there is some comparison of the models out there (in particular
> I would imagine that when developing the newer models they compared to the
> older ones), but I haven't seen an overwhelming consensus of one being
> superior to the other.
>
> Good luck!
>
> Aron
>
> On Fri, Jul 29, 2016 at 5:05 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
> wrote:
>
>> Hi Aron and Thomas,
>>
>> Thanks a lot for the discussion. I am getting started with implicit
>> solvent simulations, so this helped a lot.
>>
>> One question I have is, when you switch between NAMD and AMBER, do you
>> also switch the parameters you use (i.e. from CHARMM to AMBER)? In other
>> words, does the implicit solvent have to be compatible with the force field
>> that was used to parameterize the protein? Or could I use CHARMM parameters
>> in AMBER with reliable results (with respect to GB model)?
>>
>> Also, between OBC models I and II, is either of them recommended to be
>> "better" for peptide/water systems?
>>
>>
>> Regards,
>> Chitrak.
>>
>> On Fri, Jul 29, 2016 at 3:24 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>>
>>> 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
>>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>

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