[gmx-users] Replica Exchange for surface tension
jalemkul at vt.edu
Wed Mar 29 15:18:17 CEST 2017
On 3/29/17 9:16 AM, gozde ergin wrote:
> Are you sure it is not CHARMM36 because it is written:
> ;; Generated by CHARMM-GUI (http://www.charmm-gui.org) v1.7
> ;; psf2itp.py
> ;; Correspondance:
> ;; j712l362 at ku.edu or wonpil at ku.edu
> ;; CHARMM36 FF in GROMACS format
> on the top of the .itp files.
OK, I was thinking too quickly, the workflow goes like this: If a molecule is
identified as part of the existing force field, it is used. If it is not, then
CGenFF is called. So your SDS may be CHARMM36 but your cocobetaine is not. You
can check against the CHARMM force field files and also the atom types
themselves. If the second character is "G" then it is CGenFF, otherwise it is
Do not rely on header comments; those are often boilerplate. Check the
>> On 29 Mar 2017, at 15:06, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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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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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