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

Hector Mrz-Seara Monne hseara at netscape.net
Wed Sep 22 20:32:40 CEST 2004

Thank you Erik,
I gonna read carefully the manual in order to understand the restrains 
possibilities and try to go on in the simulation.

lindahl at sbc.su.se 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 configuration.
> 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...
> Cheers,
> Erik
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