[gmx-users] Replica Exchange for surface tension
gozdeeergin at gmail.com
Wed Mar 29 10:15:40 CEST 2017
I used CHARMM GUI Input Generator tool both for SDS and cocobetaine.
So basically the reason of not getting correct surface tension is bad parametrisation of force field.
Then I should not spend time on simulation the replica exchange.
> On 28 Mar 2017, at 22:48, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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).
>> 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 A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>> Department of Pharmaceutical Sciences School of Pharmacy Health Sciences
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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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