P.S. One think that I have found:
http://www.sciencedirect.com/science/article/pii/S0005273608001077#sec1
here I need to modify the protocol changing the direction of the
mechanistic shock towards the lateral plane of the membrane, thus
producing shear flow mimicking.
2017-07-21 10:44 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> Dear David,
>
> I am interesting in you opinion if it possible in Amber to simulate a
> flow on the surface of the membrane via adding a selectively an
> acceleration to the solvent (water) in the selected direction?
>
> Alternatively, is it possible via steered md to apply a directed force
> on the selected part of the membrane-embedded protein (its
> water-exposed loops), which should be again applied in a parallel
> direction to the membrane.
>
> Thanks!
>
> Gleb
>
> 2017-07-20 17:01 GMT+02:00 David A Case <david.case.rutgers.edu>:
>> On Thu, Jul 20, 2017, James Starlight wrote:
>>
>>> All of they refereed to the application of the steered MD protocols
>>> done in N*MD, so for me is interesting of the application of the same
>>> things in amber ... because I like amber more :-)
>>
>> Well, one can certainly do steered MD in Amber....dac
>>
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Received on Fri Jul 21 2017 - 05:00:02 PDT
