[gmx-users] Semiisotropic pressure coupling

[Justin Lemkul]

On 2/16/15 7:22 PM, shivangi nangia wrote:
> Hello Justin,
>
> I have a follow up question.
>
> The non-bonded parameters you have pointed out to :
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> is valid if the system contains only lipid or it should be use with a system
> containing lipid and protein too.
>

Those are the proper settings for anything under CHARMM36, though as I said 
earlier, it seems that proteins and nucleic acids are less sensitive to the 
differences between force-switch and potential-switch.  But what I posted on 
that page is what everyone who wants to use CHARMM36 properly *should* be doing. 
  If you don't, well, you've seen the consequences firsthand :)

-Justin

> Thanks,
>
> sxn
>
>
> On Mon, Feb 16, 2015 at 2:10 PM, shivangi nangia <shivangi.nangia at gmail.com
> <mailto:shivangi.nangia at gmail.com>> wrote:
>
>     Thanks a lot Justin!!!
>
>
>
>
>
>
>     On Sun, Feb 15, 2015 at 1:13 PM, Justin Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>         On 2/15/15 1:02 PM, shivangi nangia wrote:
>
>             Dear Justin,
>
>             Thanks for the continuous help.
>
>             Since I have done reverse CG, The CG POPC was equilibrated alone
>             anisotropically, The APL was fine there.
>             On reverse CG and NVT its still fine, it only after NPT it starts
>             dropping.
>
>
>         Of course it's fine during NVT - the box can't change so the area is
>         constant.
>
>             I am calculating APL as (2*Lx*Ly)/(No. of Lipids).
>
>
>         That's only valid for pure, symmetric membranes.  You have a protein
>         embedded in one leaflet, so this method is wrong.
>
>             You mentioned to get gull force field from your site, is it here:
>
>             http://mackerell.umaryland.__edu/charmm_ff.shtml#gromacs
>             <http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs>
>
>
>         Yes, that's the right place.
>
>             On unzipping this I see POPC is an .trp entry.
>
>             If there is some other database, kindly point it out to me.
>
>
>         What I'm telling you is to use those force field files to (1) verify
>         that your POPC parameters are right (they should be) and (2) you'll have
>         the right protein topology (there are different bonded parameters that
>         will affect protein dynamics).
>
>         Again, I must emphasize - troubleshooting the APL of this system with
>         respect to the known APL of pure POPC is pointless.  You have a protein
>         that convolutes (and potentially changes) everything.  If you want to
>         simulate pure POPC to verify that things are fine, do that.  But taking
>         more time on any perceived discrepancies here is not productive.
>
>
>         -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
>         <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>         <tel:%28410%29%20706-7441>
>         http://mackerell.umaryland.__edu/~jalemkul
>         <http://mackerell.umaryland.edu/~jalemkul>
>
>         ==============================__====================
>
>
>

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

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

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