[gmx-users] CHARMM36 lipid bilayers

Pär Bjelkmar bjelkmar at cbr.su.se
Fri Oct 22 13:12:34 CEST 2010

I'm a bit surprised that the CHARMM tip3p makes a significant difference, how large is the difference approximately?


> 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
>>>> To: 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
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the
>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> -- 
> Dr Thomas Piggot
> University of Southampton, UK.

Pär Bjelkmar, Ph.D. student		

Stockholm Center for Biomembrane Research (CBR),
Stockholm Bioinformatics Center (SBC),
Department of Biochemistry and Biophysics (DBB),
Stockholm University

Tel: 	+46-8-16 2746			
Fax: +46-8-15 3679			
E-mail: bjelkmar at cbr.su.se	
Home: http://www.dbb.su.se/User:Bjelkmar		

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101022/8be4a0a4/attachment.html>

More information about the gromacs.org_gmx-users mailing list