Hi Eric,
Indeed, and I'm looking forward to the 2014 GRC in a few months.
For the simulations you want to run here (with lipid14) is yes I suggest
using NTP=2. Just make sure the temperature you choose to run at is
reasonable for the lipids you are simulating. I.e. such that they would
not be in the gel phase.
All the best
Ross
On 5/20/14, 12:56 PM, "Eric Hill" <ehh713.gmail.com> wrote:
>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
>>>>
>>>>
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Received on Tue May 20 2014 - 14:00:03 PDT
