[gmx-users] Replica Exchange for surface tension

[Justin Lemkul]

On 3/31/17 8:13 AM, gozde ergin wrote:
> Hi Justin,
>
> I found a new optimized NBFIX parameter for SOD-Oxygen of Betaine and SOD-Oxygen of SDS.
> On the other hand since betaine is a zwitterionic molecule there is + charge on Nitrogen(N) and - charge on the Oxygen atoms and SDS is anionic there is - charge on SO4 and there is + SOD molecules inside the bulk, I also need to define NBFIX parameter between N-Oxygen of betaine and N-Oxygen of SDS.
> However I could not find them, do you have any hint how to develop new optimised NBFIX parameter these specific combination?

NBFIX parameters are used to correct overly strong/weak interactions between 
specific atom type pairs.  Generally, you need to do QM interaction energy 
calculations as a function of distance to identify the minimum energy and 
distance of that interaction.  Then compare with the stock force field values, 
and use NBFIX to correct it, if necessary.  You would not do this with full SDS 
and betaine, just some representative model compounds that contain the 
(suspected) incorrect interaction.

-Justin

> There is  2016 JCTC Yoo et.al. paper that did some optimization however they used amine groups and betaine has tetramethylamine group.
>
> Thanks in advance.
>
>
>
>>
>>
>>
>> On 3/28/17 2:59 PM, gozde ergin wrote:
>>> I use Charmm36 force field. Do you mean the force field parameter between
>>> cocobetaine and SDS? Because for pure surfactant I am able to estimate the
>>> correct surface tension. Which means force field parameter of SDS-water and
>>> cocobetaine-water is fine.
>>>
>>
>> SDS is a standard part of CHARMM36 but I have no idea what cocobetaine is.  Did you find existing parameters for it or did you do the parametrization yourself? The larger point is that you've probably stumbled upon the corner cases that often come up - some combination of parameters has never been looked at before and it requires more refinement.  If both interact with water fine but interact with each other improperly, that means either the SDS-cocobetaine interactions are too weak or too strong, or that they induce some sort of abnormal conformational sampling.
>>
>> You'll need to look at the microscopic details of how they interact - which groups are associated with which, how the conformational ensembles of each differ from those observed in water, etc.  Then you can focus on specific elements of refinement that may need to be done (e.g. NBFIX for LJ interactions that are often the culprit in such cases, and/or perhaps some sub-par dihedral parameters that lead to bad sampling when a particular interaction occurs).
>>
>> -Justin
>>
>>> Sent from my iPhone
>>>
>>>> On 28 Mar 2017, at 7:21 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 3/28/17 12:43 PM, gozde ergin wrote: I have a mixed system of SDS and
>>>>> cocobetaine on water surface. I estimated the surface tension of SDS on
>>>>> water surface and cocabetaine on surface tension separately and correctly
>>>>> (comparing with experimental results). However I could not estimate the
>>>>> correct surface tension for SDS-cocobetaine mix in even 150 ns
>>>>> simulation. Do you think replica exchange simulation would help me to
>>>>> estimate the correct surface tension of mixed system? Do you have any
>>>>> idea why I failed in estimating the mixed system surface tension?
>>>>>
>>>>
>>>> If a physical model fails to produce known physical properties, the problem
>>>> is often the model itself.  I'd suspect the force field parameters first.
>>>> What is the source of your parameters?
>>>>
>>>> Replica exchange helps you get over large barriers to improve sampling, but
>>>> I doubt that's useful here in a mixture of small molecules.
>>>>
>>>> -Justin
>>>>
>>>> -- ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>
>>>> Department of Pharmaceutical Sciences School of Pharmacy Health Sciences
>>>> Facility II, Room 629 University of Maryland, Baltimore 20 Penn St.
>>>> Baltimore, MD 21201
>>>>
>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
>>
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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================