Yes, I was surprised as well.
It depends on the value of rvdw-switch. For some systems it can be 10
A^2, for others much smaller.
Tom
Pär Bjelkmar wrote:
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.pig...@soton.ac.uk <mailto:t.pig...@soton.ac.uk>
To: gmx-users@gromacs.org <mailto:gmx-users@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.
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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: bjelk...@cbr.su.se <mailto:bjelk...@cbr.su.se>
Home: http://www.dbb.su.se/User:Bjelkmar
<><><><><><><><><><><><><><><><><><><><><>
--
Dr Thomas Piggot
University of Southampton, UK.
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