[gmx-users] Replica Exchange for surface tension

Justin Lemkul jalemkul at vt.edu
Wed Mar 29 15:07:08 CEST 2017

On 3/29/17 4:15 AM, gozde ergin wrote:
> I used CHARMM GUI Input Generator tool both for SDS and cocobetaine.

For the sake of clarity, you should understand that you are *not* then using 
CHARMM36.  CHARMM-GUI calls the CGenFF program to parametrize the molecule, so 
you are using CGenFF parameters, which are compatible with CHARMM by design, but 
are not the standard CHARMM36 parameters.  Thus your SDS model will differ from 
the standard one that we have in the lipids/detergents file.  You should compare 
it to make sure it is reasonable.  A general force field will sacrifice some 
accuracy in the name of generality and transferability.

> 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.

Indeed.  Look at the things I mentioned before.  If the model doesn't work well, 
then you have to get into the details of why.  Burning through more time hoping 
it will work out and expensive stuff like REMD is just a waste.



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


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