[gmx-users] How to performe a monolayer dynamics?

Eric Jakobsson jake at ncsa.uiuc.edu
Thu Sep 23 19:14:58 CEST 2004

A couple of other points from our experiences with membranes:

20 angstrom cut-off's are adequate.  One does see systematic difference 
between results at 15 angstroms and 20 angstroms, but not between 20 and 
25.  Our assay was the surface dipole potential, which is very sensitive 
since its magnitude depends on very subtle changes in the orientation of 

If you do use cutoffs, use neutral charge groups.  Otherwise you will 
generate artefacts in the radial distribution functions at the cutoff 
distance, even for cutoffs as long as 20 angstroms.  We have not published 
all this stuff in detail, but we did look at these issues systematically in 
order to satisfy ourselves that we were doing things right.


At 05:49 PM 9/22/2004 +0200, you wrote:
>Hi Hector,
>On Sep 22, 2004, at 4:59 PM, Hector Mrz-Seara Monne wrote:
>>First of all, let me thank in advance,
>>After reading several references about monolayers , and bilayers 
>>specially those performed by Erik Lindal and Peter Tieleman there are 
>>several things that worry me. My system isn't a tipical lipid monolayer, 
>>it is contituted by hydrocarbonated-azo-benzene with a carboxylated head 
>>and to start we want to reproduce an experimental isoterm.
>>I have charge the carboxylix acid at the end of the chain and then when I 
>>made the monolayer and run the dynamic without water, the monolayer is 
>>destroyed by the coulomb forces, as I expected.  But as I read many 
>>authors said that they start the simulation without water to allow the 
>>monomer to get a better tilt of chains. How they perform that? How were 
>>they able to maintain the heads at z=0 for afterwards insert the waters bellow?
>First, you probably don't need to worry about the chain equilibration - 
>those comments were written in the days when 10 ns was a long simulation. 
>Now it's probably easier to simulate with water until things settle.
>Second, if you choose to equilibrate without water the stability will 
>depend on the type of lipids. DPPC for instance is nice and stable even 
>without water, as long as you have it in a reasonable starting bilayer 
>Still, there are quite a few other solutions: you could add position 
>restraints to an atom in the headgroup so they can't move too much (my 
>personal favorite), or you can freeze e.g. the z coordinate of an atom 
>completely during the equilibration. The details are available in the 
>Gromacs manual.
>>Another question is that, as I know the best way of calculating couloumb 
>>forces is with PME in gromacs. That is true? Why then lots of people 
>>using gromacs use a shifted cut-off? In case of using PME I have to 
>>neutralize my system with ions ( in the hydrated monolayer)?, and in the 
>>case of using a cut-off?
>"Best" depends on your needs. It's the most accurate and only slightly 
>slower (30%), but cut-offs scale much better over high number of 
>processors in parallel runs and long cut-offs are usually a perfectly fine 
>alternative when it comes to accuracy.
>The PME algorithm works even for systems with a net charge, but due to the 
>way it is evaluated the average charge of the system is taken as the zero 
>level (grossly simplified), so it kind of corresponds to a background 
>uniform charge that neutralizes the system. Conceptually it's probably 
>easier to add counterions if you don't want to think about those effects...
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909
(Currently on leave to the National Institutes of Health in Bethesda, 
Maryland, to be Director of the NIGMS Center for Bioinformatics and 
Computational Biology and Chair of the NIH Biomedical Information Science 
and Technology Initiative Consortium, but maintaining my research lab at 
Illinois by periodic commuting.  My usual schedule is four days a week at 
NIH and three days a week at Illinois.)

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