Thanks Ben!! Your help is much appreciated. I have been using isotropic
scaling but will try with the suggested input.
Best regards,
Eric
On Tue, May 20, 2014 at 12:22 PM, Benjamin D Madej <bmadej.ucsd.edu> wrote:
> To clarify, what should be set in the input file is:
> ntp=3
> csurften=3
> gamma_ten=0.0
> ninterface=2
>
> All the best,
> Ben
> ________________________________________
> From: Benjamin D Madej
> Sent: Tuesday, May 20, 2014 11:15 AM
> To: AMBER Mailing List
> Subject: RE: [AMBER] cant run ntp=3 without csurften
>
> Eric,
>
> Actually, in the current implementation in pmemd, there is a fairly simple
> solution for semiisotropic pressure coupling:
> ntp=3
> csurften=0.0
>
> Why does this work? Starting with (in LaTex):
> \gamma = \frac{h_z}{2} (P_{zz}-\overline{P_t})
> where gamma is the surface tension, h_z is the instantaneous box dimension
> in the direction of surface tension, P_{zz} is the pressure in the
> direction of surface tension, P_t is the average tangential pressure.
>
> reduces to the semiisotropic coupling when there is no surface tension. If
> my math is correct, then:
> \gamma = 0
> means
> P_{zz} = \overline{P_t} = \frac{P_{xx} + P_{yy}}{2}
> Where P_{xx} and P_{yy} are the tangential components of pressure. In
> pmemd, this constraint works by setting P_{xx} = P_{yy} and solving for
> P_{xx}.
>
> It is an additional constraint that removes one degree of freedom from the
> simulation. Lipid14 simulations were run with *anisotropic* pressure
> coupling.
>
> It depends on the lipid bilayer system that you're trying to simulate.
> It's possible on very long timescales that bilayer system may not be stable
> and will collapse in one dimension (i.e. the box dimension decreases
> significantly and the simulation stops). If that is a major problem with
> your simulations, you may want additional semi-isotropic coupling. It's
> definitely something to take note of in these bilayer simulations.
>
> All the best,
> Ben Madej
> UCSD Chemistry and Biochemistry
> SDSC
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: Tuesday, May 20, 2014 10:11 AM
> To: amber.ambermd.org
> Subject: Re: [AMBER] cant run ntp=3 without csurften
>
> On Tue, 2014-05-20 at 10:48 -0600, Eric Hill wrote:
> > Hi Amber devs,
> > Now that lipid14 is published, I was wondering if you had a suggestion
> > to work around the following issue: Amber requires that csurften be set
> > for ntp=3 (semiisotropic coupling). This would be nice to use in my
> > membrane simulations. If there is a workaround possible, it would be
> > great to know.
>
> I think the appropriate workaround is to just use anisotropic pressure
> scaling. The semi-isotropic barostat seems like a hack to me to correct
> for deficiencies in the force field (as is the constant surface tension
> term). Since Lipid14 no longer needs constant surface tension, it
> likely does not need semi-isotropic coupling, either.
>
> If your system is truly isotropic, an anisotropic barostat will result
> in isotropic scaling on average. Likewise, if your system is truly
> semi-isotropic (like you would hope for an ideal layer), the anisotropic
> barostat will result in semiisotropic scaling on average.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue May 20 2014 - 12:00:03 PDT
