[gmx-users] lipids per area charmm36 popc

[David van der Spoel]

On 2011-05-19 00.31, Thomas Piggot wrote:
> I agree with Justin, 1 ns is just nowhere near long enough. Something in
> the tens of ns should do it.
>
> I have used pretty much the same settings as you (using the CHARMM
> water, as you have) and get APL's matching those published in the Klauda
> paper. You are correct that you should not use the dispersion
> correction, this was discussed in their paper.

And I heard some rumours that you have to use constraints = h-bonds only 
to get the right lipid phase, but that may have been for DPPC which is 
more critical AFAIK.

>
> Cheers
>
> Tom
>
> On 18/05/11 23:20, Justin A. Lemkul wrote:
>>
>> Peter C. Lai wrote:
>>> Hello
>>>
>>> I am trying to equilibrate from scratch a 196 POPC bilayer using Tom's
>>> charmm36.ff. My box has a lot of TIPS3P (charmm) waters above and below
>>> the membrane with a box size around 8.5x8.5x12.7. My desired end state
>>> is to only use the setup for g_membed but I'd also like to get a
>>> pristine
>>> tall bilayer that might be useful for other things or colleagues. I ran
>>> 1ns NPT so far with:
>>>
>>> dt = 0.002
>>>
>>> continuation = yes
>>> constraint_algorithm = lincs
>>> constraints = all-bonds
>>> lincs_iter = 1
>>> lincs_order = 4
>>> ns_type = grid
>>> nstlist = 5
>>>
>>> rlist = 1.2
>>> rlistlong = 1.4
>>> rcoulomb = 1.2
>>> rvdw = 1.2
>>> vdwtype = switch
>>> rvdw_switch = 0.8
>>> coulombtype = PME
>>> pme_order = 4
>>> fourierspacing = 0.16
>>>
>>> tcoupl = Nose-Hoover
>>> tc-grps = POPC SOL
>>> tau_t = 0.5 0.5
>>> ref_t = 300 300
>>> pcoupl = Parrinello-Rahman
>>> pcoupltype = semiisotropic
>>> tau_p = 4
>>> ref_p = 1.01325 1.01325
>>> compressibility = 4.5e-5 4.5e-5
>>> DispCorr = no
>>> comm_mode = Linear
>>> comm_grps = POPC SOL
>>>
>>> The metrics look roughly stable:
>>> Energy Average Err.Est. RMSD Tot-Drift
>>> ---------------------------------------------------------------------
>>> Temperature 300 0.00018 0.957697 0.000466096 (K)
>>> Density 1017.26 0.24 1.5953 1.4803 (kg/m^3)
>>> Pressure 1.00795 0.065 99.5783 -0.0431925 (bar)
>>> Box-X 8.58491 0.036 0.0773839 -0.235388 (nm)
>>> Box-Y 8.59611 0.036 0.0774849 -0.235696 (nm)
>>> Box-Z 12.4357 0.1 0.216337 0.659896 (nm)
>>>
>>> My APLs are ~10A^2/lipid above what they "should be" according to Klauda
>>> and experimental (I get 76-77A^2/lipid vs 65-58A^2/lipid). I suppose
>>> with TIPS3P water, I could get closer LJ packing if I turned on DispCorr
>>> but I thought that you generally left that off in charmm36 bilayer
>>> runs...
>>>
>>> Now, I also could extend for several ns until density/box drift gets
>>> smaller, but any other thoughts (yes this is probably a continuation
>>> of the
>>> CHARMM36 lipid bilayers thread from October
>>> (http://www.mail-archive.com/gmx-users@gromacs.org/msg34582.html)?
>> Later in this thread it is suggested that one use TIPS3P ("CHARMM
>> TIP3P") water,
>> so start there, although that discussion found that the APL was
>> consistently
>> underestimated, not overestimated, as is your case.
>>
>> 1 ns is not nearly enough to make solid conclusions about membranes.
>> Lipid
>> rotational relaxation is on the order of 5 ns, and translational
>> relaxation
>> about 10 ns. I'd say you need at least 20 ns of simulation to make any
>> real
>> conclusions, with some of that of course discarded as equilibration.
>>
>> -Justin
>>
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se