[gmx-users] mdp-settings for charmm36 and lipid apl values
Patrick Fuchs
patrick.fuchs at univ-paris-diderot.fr
Fri May 10 09:58:00 CEST 2013
Hi,
in addition to Chris' comments, I think one good way for getting APL of
a lipid mixture is the one proposed by Edholm and Nagle :
http://www.cell.com/biophysj/abstract/S0006-3495%2805%2972827-7.
The idea is to run simulations at different concentrations of [A] and [B].
Ciao,
Patrick
Le 09/05/2013 01:06, Christopher Neale a écrit :
> It is a really bad idea to use standard tip3p with charmm36 lipids (see the Piggot paper that you referenced and also Sapay, N. et al. 2010 J. Comp. Chem. 32, 1400-1410 + probably others).
>
> dt 0.001 with nstlist 5 seems like overkill on the nstlist update frequency (not a problem though).
>
> Here's how I do charmm36 lipid simulations:
>
> constraints = all-bonds
> lincs-iter = 1
> lincs-order = 6
> constraint_algorithm = lincs
> integrator = sd
> dt = 0.002
> tinit = 0
> nsteps = 5000000
> nstcomm = 1
> nstxout = 5000000
> nstvout = 5000000
> nstfout = 5000000
> nstxtcout = 50000
> nstenergy = 50000
> nstlist = 10
> nstlog=0 ; reduce log file size
> ns_type = grid
> vdwtype = switch
> rlist = 1.2
> rlistlong = 1.3
> rvdw = 1.2
> rvdw-switch = 0.8
> rcoulomb = 1.2
> coulombtype = PME
> ewald-rtol = 1e-5
> optimize_fft = yes
> fourierspacing = 0.12
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> pme_order = 4
> tc_grps = System
> tau_t = 1.0
> ld_seed = -1
> ref_t = 310
> gen_temp = 310
> gen_vel = yes
> unconstrained_start = no
> gen_seed = -1
> Pcoupl = berendsen
> pcoupltype = semiisotropic
> tau_p = 4 4
> compressibility = 4.5e-5 4.5e-5
> ref_p = 1.0 1.0
>
>
> For a pure POPC bilayer with Charmm36 lipids and tips3p water, I get ~ 0.64 nm^2/lipid (not using grid-mat, just looking at box dimensions).
>
> If I use regular tip3p instead, the APL decreases a lot and eventually forms a gel. In simple terms of APL and phase, you can get the same results as tips3p (0.64 nm^2/lipid) if you use tip4p (and spce is not too bad, but is still not as close as tip4p). Note tip4p will run faster than tips3p by a large margin. Nevertheless, I use tip3sp in all of my work with charmm36.
>
> Also, note that ions can shrink your APL, particularly Na+ (and divalent cations are even worse). My simulations use 50 mM KCl, which basically doesn't affect the average APL (although 50 mM NaCl does noticeably reduce the APL).
>
> Finally, I am not convinced that a per-molecule area per lipid is a useful quantity to compare to experimental areas per lipid. I haven't looked at Grid-Mat myself, but there must be a lot of assumptions underlying any analysis that tried to assign an "area" to a single 3D lipid. If I were you, I'd be looking for expt. results of APL for POPC vs. POPE vs. 70%POPC/30%POPE. Also, are you entirely sure that you didn't mix up the POPC vs. POPE values? It looks to me like a simple labelling error enough that it warrants a second look.
>
> Chris.
>
>
>
> -- original message --
>
> I've been experimenting with simulations of mixed bilayers (512 lipids in
> total, 70% POPC, 30% POPE) using the charmm36 parameter set in gromacs, and
> have a couple of questions. I know this has been discussed before, but I'd
> appreciate some input nonetheless :-)
>
> The relevant sections of my mdp-file are pasted below:
>
> ; Start time and timestep in ps
> tinit = 0
> dt = 0.001
> nsteps = 100000000
>
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist = 5
> ; ns algorithm (simple or grid)
> ns_type = grid
> ; Periodic boundary conditions: xyz, no, xy
> pbc = xyz
> periodic_molecules = no
> ; nblist cut-off
> rlist = 1.2
> ; long-range cut-off for switched potentials
> rlistlong = 1.4
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype = PME
> rcoulomb-switch = 0
> rcoulomb = 1.2
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r = 1
> epsilon_rf = 1
> ; Method for doing Van der Waals
> vdw-type = switch
> ; cut-off lengths
> rvdw-switch = 0.8
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = No
>
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling
> tcoupl = V-rescale
> nsttcouple = -1
> nh-chain-length = 10
> ; Groups to couple separately
> tc-grps = System
> ; Time constant (ps) and reference temperature (K)
> tau_t = 0.1
> ref_t = 300
> ; Pressure coupling
> pcoupl = Parrinello-Rahman
> pcoupltype = semiisotropic
> nstpcouple = -1
>
> This is as far as I can tell from earlier discussions on the list, and also
> from reading the Piggott et al. paper in JCTC, the correct settings for
> charmm36.
>
> After a simulation of ~50 ns, I use GridMatMD to calculate the area per
> headgroup of POPC and POPE, respectively, and get what I think are not 100%
> acceptable results (but maybe they are)
>
> For POPC, I get 59,7 A^2, and for POPE, I get 63,1 A^2.
>
> The value for POPE would have been fine I suppose if it hadn't been for the
> fact that the APL for POPC is smaller. Should it not be larger than POPE?
>
> I notice in the Piggott-paper that they in the supplement for some
> simulations of POPC also get APL's of around 59-60 (without POPE of
> course), and that the results depend to some extent also on the usage of
> TIP3P vs TIP3SP water models. I have been using "normal" TIP3P here.
>
> Could anyone comment on (a) my mdp-file settings, and (b) the resulting
> APL, and tell me if I should be worried about anything?
>
> THANKS
>
--
_______________________________________________________________
Patrick FUCHS
Dynamique des membranes et trafic intracellulaire
Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot
Bâtiment Buffon, 15 rue Hélène Brion, 75013 Paris
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