[gmx-users] gromacs.org_gmx-users Digest, Vol 170, Issue 27

[Muthukumaran Rajagopalan]

thank you for the reply Justin.

though the APL looks close to the acceptable range, I am afraid the SN1 and SN2 acyl chain parameters are not in the range as reported by  Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903 and also the membrane thickness increases.  
 

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> Message: 3
> Date: Tue, 5 Jun 2018 19:08:45 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] mdp-settings for charmm36 and lipid apl
> 	values
> Message-ID: <8f727384-96db-e744-73b8-b1f2bbe718ff at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> 
> 
> On 6/5/18 1:03 PM, Muthukumaran Rajagopalan wrote:
> > Dear Gromacs Users,
> >
> >
> > I have recently started performing membrane simulations in gromacs 5.01 version, I have started running simulations with pure POPE bilayer constructed from charmm-gui membrane builder with XY dimension 70 angs (84 lipids in each bilayer). The bilayer is solvated with 0.15 mol of KCL ( as Na ions have problem with lipid layers). The lipid layer is solvated with hydration number of 36 (lipid:water ratio).
> >
> >
> > I went through a series of literature and gromacs mailing list regarding decrease in area per lipid and tried different combinations but the area per lipid decreases by 3-4 angs from the experimental values (~58 for POPE).
> >
> >
> > I have referred Pluhackova, K et al J. Phys. Chem. B 2016, 120, 3888?3903
> 
> The APL value they obtained was 55.5 A^2, so your observations are 
> consistent. The force field apparently underestimates APL slightly.
> 
> -Justin
> 
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> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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-- 
with regards 

R. Muthukumaran