[AMBER] umbrella sampling process

From: <krishna.2015.iitg.ernet.in>
Date: Wed, 17 Jan 2018 23:34:33 +0530

Dear all,

I want to conduct umbrella sampling simulations in AMBER14 involving a
single molecule and a homo-dimer of that molecule to explore the
energy cost of growing clusters from dimers. That means the system
will contain 3 monomer of same molecules out of which 2 monomers will
be engaged to form that dimer. In this case, firstly, I have to fix at
an equilibrium distance to maintain the dimer for all of the umbrella
windows. And secondly, a distance needs to be fixed between the center
of a mass of a third molecule and the center of mass of one of the
molecules in that dimer. Then I want to vary this distance between COM
of dimer and COM of the monomer between 2 to 12 A. Is it possible?
If it is possible then what is the procedure to perform this
simulation? And what about the input files? Kindly help.


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Received on Wed Jan 17 2018 - 10:30:02 PST
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