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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> > AMBER.ambermd.org
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>
>
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Received on Tue Jul 17 2012 - 17:00:02 PDT
