[gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

[Peter C. Lai]

On 2012-07-23 02:34:31PM -0300, Sebastien Cote wrote:
> 
> There is not much difference when using DispCorr or not. At least on the same time scale as the simulation with switch cutoff from 0.8 to 1.2 nm and on the same time scale. 
> 
> Should DispCorr be used in all membrane simulations? I thought that we should always use this correction. 

I alwasy thought it was actually forcefield dependent. I never use it with 
CHARMM since the mdp files I used as the basis for mine didn't with C27, and 
I get acceptable APL with POPC when using the same mdp with C36. I haven't 
compared the codes for CHARMM to see if dispcorr is builtin to the gromacs 
implementation or not, but the reason I brought it up is that on past 
mailing list discussions about TIPS3P, there were reports of significant
density differences with and without dispcorr.


> 
> Thanks, 
> 
> Sebastien 
> 
> ----------------------------------------
> > Date: Fri, 20 Jul 2012 12:47:44 -0500
> > From: pcl at uab.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?
> >
> > Did you play with DispCorr?
> >
> > On 2012-07-20 09:46:13AM -0300, Sebastien Cote wrote:
> > >
> > > Dear Gromacs users,
> > >
> > > My simulations on a POPE membrane using the CHARMM36 parameters are giving ''area per lipid'' values well below the experimental value (59.75-60.75 Angstroms2). Is their someone else experiencing a similar problem? If yes, how did you solved it?
> > >
> > > I did the following :
> > >
> > > I used the CHARMM36 parameters kindly provided by Thomas J. Piggot on the Users contribution section on Gromacs website.
> > > My starting configuration was taken from : http://terpconnect.umd.edu/~jbklauda/research/download.html
> > > It is a POPE membrane of 80 lipids equilibrated in NPT at T=310K and P=1atm for 40 ns. It is taken from the article Klauda, J. B. et al. 2010 J. Phys. Chem. B, 114, 7830-7843.
> > >
> > > At first, I tested normal TIP3P vs. CHARMM TIP3P and saw that normal TIP3P gives smaller Area per lipid of about 2-3 Angstroms. This was also observed by T.J. Piggot (personnal communication) and Tieleman (Sapay, N. et al. 2010 J. Comp. Chem. 32, 1400-1410). So, I will present only the simulations using CHARMM TIP3P. As in Klauda's paper, my simulations are at 310K and 1 atm. As them, I used a switch cutoff for vdw, and I used normal cutoff for PME. The simulations are 20 ns. I can send my .mdp file for more details. I varied the switch condition on vdw :
> > >
> > > 1- For a switch from 0.8 to 1.2 (as in Klauda's paper), I got Area per lipid of about 56.5 Angstroms2; whereas they got 59.2 in their paper, matching the experimental value of 59.75-60.75.
> > > 2- For a switch from 1.0 to 1.2, I got Area per lipid of about 53.5 Angstroms2, which is smaller than the previous cutoff. This is surprising since a previous thread on gromacs-users mailing lists said that increasing the lower cutoff, increased the Area per lipid or had not impact on POPC of DPPC.
> > > 3- For a switch from 1.1 to 1.2, I got Area per lipid of about 55 Angstroms2.
> > > 4- For a hard cutoff at 1.4, I got Area per lipid of about 52 Angstroms2.
> > >
> > > I also tried to re-equilibrate the membrane in the NPAT ensemble for 10 ns at 310K and 1 atm. Then, when I launched the simulation in NPT, I ended up with different results :
> > >
> > > 1- Switch from 0.8 to 1.2 gave a smaller area per lipid of 54 Angstroms2.
> > > 2- Switch from 1.0 to 1.2 gave a larger area per lipid of 55 Angstroms2.
> > > 4- Hard cutoff at 1.4 gave a similar area per lipid of 52.5 Angstroms2.
> > >
> > > I looked at the POPE paramaters for CHARMM36 in Gromacs, and they agree with the published parameters.
> > >
> > > Am I doing anything wrong? Is their someone else experiencing a similar problem for POPE? If yes, how did you solved it?
> > >
> > > Should I instead use CHARMM27 parameters in the NPAT ensemble? I want to study the interaction between a peptide and the POPE membrane. I am troubled that the NPAT ensemble might influence my results in a bad way. Also, I can not use OPLS AA nor GROMOS for the protein interactions because these force fields are not giving the correct structural ensemble for my peptide in solution.
> > >
> > > I am willing to send more information if you need.
> > >
> > > Thanks a lot,
> > > Sincerely,
> > >
> > > Sébastien --
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> > --
> > ==================================================================
> > Peter C. Lai | University of Alabama-Birmingham
> > Programmer/Analyst | KAUL 752A
> > Genetics, Div. of Research | 705 South 20th Street
> > pcl at uab.edu | Birmingham AL 35294-4461
> > (205) 690-0808 |
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-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================