From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Mon Dec 26 2005 - 10:52:40 CST
ABF and umbrella sampling are altogether two different approaches to
the determination of free energy profiles (see Darve and Pohorille,
J. Chem. Phys. 2001, 115, 9169-9183 and Hénin and Chipot, J. Chem. Phys.
2004, 121, 2904-2914).
If I understand you correctly, you are interested in the free energy
profile characterizing the translocation of your complex across the
In a previous message, I explained how to define your reaction
coordinate, using the COM of the water lamella as a reference.
You may define a pseudo-COM of the complex based on a small
number of atoms, paying attention that neither be directly
involved in a constrained bond - or alternatively including
the hydrogen atoms of the frozen bonds in your list of atoms.
For efficiency purposes, you may want to break your reaction path
into sequential, non-overlapping windows. To avoid sampling to
"spill" beyond the limits of these windows, apply an appropriate
force constant - 100 kcal/mol/Å² should be fine (see Hénin and Chipot,
J. Chem. Phys. 2005, 123).
Manori Indira Jayasinghe wrote:
>Thank you for your comments and I think I need to figure out the proper values for these variable to suit my system.I will give some details of what I am doing. I am simulating a freenergy profile of a molecular complex with 100 atoms namely Uranyl Nitrate Tri Butyl Phosphate at water (874)/hexane(143) interface. In my system I have 3 interfaces, water/water vapor, water/hexane, hexane/hexane vapor.I use mmfp in charmm to prevent hexane and water penetrating out of the unit cell. But I havent done anything like that in namd.I am running this system in Charmm Umbrella sampling module and it runs fine except one problem. RXNCOR in charmm is not recomended for parallel runinng and it take for one window 3 Angstrom for 500 ps about 2 and half days, which is qiute long I think . I use 0.7 Kcal/mole for the force constant in RXNCOR.I was able to do 2 windows for 500 ps each the free enrgy profiles looks fine. I need to switch my system to namd abf, hence I can get it run parallel and my simulation will be faster.Do you have any sujestions for those variables.
>Thank you very much. Manori
Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Université Henri Poincaré - Nancy 1 Phone: (33) 3-83-68-40-97
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