Yes, that is correct-- two layers of phospholipids to a bilayer.
Ben Madej
Walker MD Lab
________________________________________
From: Albert [mailmd2011.gmail.com]
Sent: Tuesday, July 17, 2012 10:52 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER12 - ninterface for double bilayer system
hi Ben
thanks for kind comments.
did you mean single BI-layer which still contains two layer lipids,
right? probably the question is naive, but i just want to be sure.
2012/7/18, Benjamin Madej <bmadej.ucsd.edu>:
> Albert,
>
> ninterface = 2 for a single bilayer with surface tension. ninterface = 4
> for
> two bilayers with surface tension. gamma_ten will not be the same with one
> bilayer vs. two bilayers.
>
> Ben
>
> -----Original Message-----
> From: Albert [mailto:mailmd2011.gmail.com]
> Sent: Monday, July 16, 2012 10:10 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] AMBER12 - ninterface for double bilayer system
>
> Hi Ben:
> in the manual it is said ninterface=2 for the single bilayer. Do you
> think
> it is necessary to increase this value for it when we use surface tension?
>
> thank you very much.
> Albert
>
> 2012/7/17 Benjamin Madej <bmadej.ucsd.edu>
>
>> James,
>>
>> Ninterface should be set to the number of interfaces in your system.
>> In your case, it should be ninterface = 4. Basically, surface tension
>> is implemented into the pressure coupling in such a way that the
>> reference surface tension value, 'gamma_ten', is divided by the number
>> of interfaces in the calculation of the reference pressure for
>> pressure coupling.
>>
>> For some initial reading on constant surface tension, I suggest Zhang, Y.
>> et
>> al. J. Phys. Chem. 1995 and Feller, et al. J. Phys. Chem. 1995.
>>
>> I don't know what reference surface tension value to use for your
>> system. I think it will be larger than a single bilayer, but it won't
>> necessarily be twice a single bilayer system's surface tension.
>>
>> I know this type of system has been done before using other force fields.
>> However, our group has not tested multiple interfaces in a system like
>> you describe. I am also interested in how this system behaves.
>>
>> Ben Madej
>> Walker Molecular Dynamics Lab
>>
>> -----Original Message-----
>> From: Ross Walker [mailto:ross.rosswalker.co.uk]
>> Sent: Monday, July 16, 2012 10:59 AM
>> To: 'AMBER Mailing List'
>> Subject: Re: [AMBER] AMBER12 - ninterface for double bilayer system
>>
>> Hi James,
>>
>> Ben Madej might be able to comment more here since he was the one who
>> implemented the constant surface tension code. My understanding is
>> that setting the number of interfaces to 4 should be sufficient - it
>> is basically a scale factor for the actual surface tension value.
>>
>> That said I don't think we have ever actually tried multiple bilayers
>> so this will definitely be an experiment. I believe the surface
>> tension should probably just be the same as a single bilayer but of
>> course that will depend if the distance between the bilayers is small
>> such that there is substantial interaction between the two. Either way
>> I'd be interested to hear what you find when you actually try it.
>>
>> All the best
>> Ross
>>
>> > -----Original Message-----
>> > From: James Murdock [mailto:james.murdock.86.gmx.com]
>> > Sent: Monday, July 16, 2012 3:31 AM
>> > To: amber.ambermd.org
>> > Subject: [AMBER] AMBER12 - ninterface for double bilayer system
>> >
>> > Dear Amber users,
>> >
>> > I'm currently interested in the simulation of a system composed by
>> > two bilayers separated by a water slab between those two bilayers
>> > and with water slabs on the simulation cell boundaries. As I intend
>> > to use LIPID11, a surface tension dependent FF for this system, I
>> > believe that the ninterface value should be adjusted accordingly to
>> > the number of water/lipid interfaces, following the statement on
>> > page 26 of the
>> > AMBER12 manual:
>> >
>> > ninterface
>> > Number of interfaces in the periodic box. There must be at least
>> > two interfaces in the periodic box. Two interfaces is appropriate
>> > for a lipid bilayer system and is the default value.
>> > So, if for a single bilayer system ninterface = 2, then for a double
>> > bilayer system ninterface = 4. What are your thoughts concerning
>> > this change?
>> > I am yet to discover if the surface tension value should be changed
>> > from the value appropriate for a single bilayer system.
>> >
>> > Regards,
>> > JM
>> > _______________________________________________
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Received on Tue Jul 24 2012 - 08:00:04 PDT
