jalemkul at vt.edu
Wed Oct 31 19:30:40 CET 2018
On 10/31/18 2:25 PM, ABEL Stephane wrote:
> Just my 2 cents
> If I recall well CHARMM36 and others force fields (such as lipid14) were initially parametrized and validated using the anisotropic pressure
True, but only for a few tens of nanoseconds in the case of C36. The
pressure coupling specification is not strictly tied to the force field.
> coupling scheme. So it make sense to use it instead of semi-isotropic pressure coupling. Moreover I found that if the membrane system is well equilibrated (for instance > 100 ns of NPT is semiisotropic for POPC or DOPC membranes), you can switch safely to anistropic pressure scheme and does not observe significant deformations of the bilayer. These observations are based on my simulations and are of course not general?
Anisotropic coupling doesn't make sense to me for membranes (though it
was used routinely years ago, as you note). The lateral properties of a
membrane are not different in x and y (assuming the bilayer normal is
along z, per convention). Hence, semiisotropic coupling is the most
defensible. I have seen simulations of less than 100 ns distort quite a
bit, though the importance of such behavior (square becoming a
rectangle, but everything still satisfying the minimum image convention)
is not clear.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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