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 Mon Jul 16 2012 - 22:30:02 PDT
