Hi Eric,
To expand on Ben's answer a little bit.
If you don't specifically have a specific reason for wanting to run with
semi-anisotropic scaling you should just set ntp=2 (anisotropic scaling)
and not specify any csurften.
Semi-anisotropic scaling was originally added because lipid11 required a
constant surface tension term to give correct lipid phases. Lipid14 was
specifically designed NOT to need a constant surface tension term and thus
should be run with ntp=2. (What Ben is suggesting is a hack to fix the
equivalence the box size in the XY dimension. You shouldn't do this unless
you have a specific reason for wanting to do it).
So for you standard Lipid14 simulation just set ntp=2.
All the best
Ross
On 5/20/14, 11:40 AM, "Eric Hill" <ehh713.gmail.com> wrote:
>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 - 13:00:02 PDT
