Re: [AMBER] umbrella sampling process

From: Andreas Tosstorff <>
Date: Wed, 17 Jan 2018 19:22:50 +0100

Hi Krishna,

have a look at the tutorials on the Amber website. There you can see
some umbrella sampling examples.



On 01/17/2018 07:04 PM, wrote:
> 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.
> thanks
> krishna
> _______________________________________________
> AMBER mailing list

M.Sc. Andreas Tosstorff
Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
Department Pharmazie
LMU München
Butenandtstr. 5-13 ( Haus B)
81377 München
Tel.: +49 89 2180 77059
AMBER mailing list
Received on Wed Jan 17 2018 - 10:30:03 PST
Custom Search