[gmx-users] CHARMM36 lipid bilayers

Fri Oct 22 16:45:46 CEST 2010

Hi there,

Tom, many thanks for your valuable suggestions. I am also surprised by
this large influence. For DPPC the change is about 5 A^2 (same settings
but different water model).

Cheers,
Sven

Pär Bjelkmar schrieb:
> I'm a bit surprised that the CHARMM tip3p makes a significant
> difference, how large is the difference approximately?
>
> /Pär
>
>> Hi Sven,
>>
>> Yes I have tested values of rvdw-switch and (unlike in your test) have 
>> seen a large impact of the area per lipid. Indeed this can also be seen 
>> in the Klauda paper where they show a decreased area per lipid (~63 A^2 
>> to ~58 A^2) in the NAMD DPPC simulations (see the graph in the 
>> Supporting Info) using a 1.1 nm cut-off for the switching compared to 
>> the 0.8 nm cut-off in their CHARMM simulations.
>>
>> I would suggest sticking to a rvdw-switch of 0.8 nm and using the CHARMM 
>> tip3p water. This gives me the closest results in terms of area per 
>> lipid for both POPC and DPPC compared to both the Klauda paper (CHARMM 
>> results) and experiment.
>>
>> Cheers
>>
>> Tom
>>
>> Sven Jakobtorweihen wrote:
>>> Hi there,
>>>
>>> Tom, thanks for this hint, yes, that is an improvement. I am looking
>>> forward to your paper. Berk, I am using switch for vdw. Although for my
>>> taste switching from 0.8 to 1.2 was quite large, I used it because the
>>> charmm paper used these values. But I just realized that the
>>> implementation of the switch is different in gromacs and charmm, I
>>> should have seen that earlier. I think I will increase rvdw_switch to
>>> 1.0. However, a couple of days ago I tested already the influence of the
>>> switching region and it wasn't dramatic, at least for the test case.
>>> Nevertheless, matching the settings used in the parametrization is
>>> always advisable. Tom, do you have tested any cutoff settings?
>>>
>>> Cheers,
>>> Sven
>>>
>>> Berk Hess schrieb:
>>>> Hi,
>>>>
>>>> Another comment on your interaction settings.
>>>> You did not mail if you are using shift or switch for vdw.
>>>> But I guess that both probably don't match exactly what Charmm does.
>>>> Since the switching range is so long and this is where a large part
>>>> of the dispersion attraction acts, this might have a large effect on
>>>> the area.
>>>>
>>>> Berk
>>>>
>>>>> Date: Thu, 21 Oct 2010 16:47:21 +0100
>>>>> From: t.piggot at soton.ac.uk <mailto:t.piggot at soton.ac.uk>
>>>>> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>>>> Subject: Re: [gmx-users] CHARMM36 lipid bilayers
>>>>>
>>>>> Hi Sven,
>>>>>
>>>>> I have also seen similar things from the area per lipid of the
>>>>> bilayers
>>>>> I have run (POPC and DPPC). I would suggest you try running with the
>>>>> CHARMM TIP3P water (tips3p.itp) and see if you get values which are
>>>>> closer to the ones published in the paper you mention. This will be
>>>>> discussed in a paper which we hope to have published fairly soon.
>>>>>
>>>>> Cheers
>>>>>
>>>>> Tom
>>>>>
>>>>> Sven Jakobtorweihen wrote:
>>>>>> Dear gmx-users,
>>>>>>
>>>>>> recently Pär Bjelkmar and Thomas Piggot have generated force field
>>>> files
>>>>>> for Charmm36 lipids. I run some simulations to find the best run
>>>>>> parameters and to check if the results of the original Charmm36 lipid
>>>>>> article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be
>>>>>> reproduced with gromacs.
>>>>>>
>>>>>> I run 40 ns NPT simulations with semiisotropic pressure coupling
>>>>>> (Parrinello-Rahman, tau_p=5), the first 10 ns are equilibration and
>>>>>> averages were calculated for the last 30 ns. DMPC and POPC at 303
>>>> K and
>>>>>> DPPC at 323.15 K (Nose-Hoover, tau-t= 1). The itp files were made
>>>>>> with
>>>>>> pdb2gmx -nochargegrp. All simulations contained 128 lipids and
>>>>>> approximately the same water/lipid ratio (water is TIP3P) as
>>>>>> Klauda et
>>>>>> al. I started from charmm27 bilayers provided at the Chramm Gui
>>>> website.
>>>>>> I used the following parameters:
>>>>>>
>>>>>> rvdw=1.20; rvdw_switch=0.80; DispCorr=No; coulombtype= PME;
>>>>>> rcoulomb=1.00; fourierspacing=0.15; pme_order=6;
>>>>>> rcoulomb_switch=0.00;
>>>>>> nstlist=10; rlist=1.00; rlistlong=1.40; constraints= hbonds; dt=
>>>>>> 0.002
>>>>>>
>>>>>> These simulations result in the following area per lipid [A^2/lipid]:
>>>>>> DMPC=56.6 +/- 0.4 ; POPC =61.8 +/- 0.4 ; DPPC=55.0 +/- 0.7
>>>>>>
>>>>>> Comparing to the results of Klauda et al (all simulation with the
>>>>>> charmm-package, except one):
>>>>>> DMPC=60.8 +/- 0.2 ; POPC=64.7 +/- 0.2 ; DPPC=62.9 +/- 0.3 ; DPPC=59.1
>>>>>> +/- 0.4 (with NAMD)
>>>>>>
>>>>>> It is obvious that my simulations with gromacs 4.5.1 give lower areas
>>>>>> per lipid for all cases. Considering the deviations observed by
>>>>>> Klauda
>>>>>> et al. between Charmm and NAMD simulations ( rvdw_switch was only
>>>>>> changed slightly in NAMD) could lead to the conclusion that DMPC and
>>>>>> POPC are fine. But I am a bit worried about the DPPC result. Did
>>>> anyone
>>>>>> have suggestions how to improve it? Are these differences expected
>>>> when
>>>>>> comparing gromacs and charmm simulations? Did by any chance
>>>> someone else
>>>>>> tested charmm36 bilayers in gromacs?
>>>>>>
>>>>>> Thanks,
>>>>>> Sven
>>>>> --
>>>>> Dr Thomas Piggot
>>>>> University of Southampton, UK.
>>>>>
>>>>> --
>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>> <mailto:gmx-users at gromacs.org>
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>>
>> -- 
>> Dr Thomas Piggot
>> University of Southampton, UK.
>
>
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>
> Pär Bjelkmar, Ph.D. student
>
>
> Stockholm Center for Biomembrane Research (CBR),
>
> Stockholm Bioinformatics Center (SBC),
>
> Department of Biochemistry and Biophysics (DBB),
>
> Stockholm University
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> Tel:  +46-8-16 2746
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