Hi Dr. Walker,
Good to hear from you, it was good to see you at the 2012 gordon
conference. I am doing simulations of "peptide" aggregation and trying
to see if insertion can spontaneously occur on the us timescale with
GPUs + lipid14. If you think that it is better to just run ntp=2 then I
will switch them back to that. Thanks for your response.
Best regards,
Eric
On 5/20/2014 1:24 PM, Ross Walker wrote:
> 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
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Tue May 20 2014 - 13:00:03 PDT
