[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/15/15 11:40 AM, Justin Lemkul wrote:
>
>
> On 2/15/15 11:32 AM, shivangi nangia wrote:
>> Sorry about that.
>>
>> Here it is:
>> https://drive.google.com/file/d/0B9SJqGLyLrwVcThWbEthaFo3SGc/view?usp=sharing
>>
>
> So this is actually a system in which a peptide is peripherally bound to a POPC
> membrane.  That complicates things significantly.  Not only is it less
> straightforward to calculate APL, but you have to consider that the protein
> itself perturbs the lipid properties.  If you want to evaluate the validity of
> the parameters, you need to be running a simulation of a pure POPC membrane.
>
> How have you calculated APL?  Have you run a pure POPC membrane simulation?
> These are the only things worth spending time on.  Otherwise, all you're seeing
> is either (1) a problem with how you're calculating APL and/or (2) effects of
> the peptide.
>

Also, it looks like the "CHARMM36" files you are using come from the GROMACS 
download site, which come from Tom's work.  He has since clarified that those 
force field files are CHARMM36 lipids only, therefore the protein parameters are 
CHARMM22/CMAP, thus not the self-consistent CHARMM36 force field that our lab 
produces.  You could be getting artifacts there, as well, though I can't 
specifically say offhand what those might be.  But the files from the GROMACS 
site should be used ONLY for pure lipid simulation.  For anything else, get the 
full force field from our site.

-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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