xu zhijun wrote:
Hi gromacs-users,
I have carefully checked the manual about the define the A and B states
for the calcualtion of free energy. And I also known that
"couple-moltype“ and "couple-lambda0" and "couple-lambda1".
However I have two types of molecules for decoupling in the simulaiton.
It seems that Gromacs can not deal with more than one tpes of moleucle
with the "couple-moltype".
For example I want to decouple the Na+ and Ca+. Is the the other way to
define the decoupling molecules? It seems that I can directly define the
B state in the top files for these two ions, repectively. If it is
reasonable, does the other molecules without the descrption of the B
state keep fixed? (I mean these molecuse will not involve the decoupling
process in the simulation.)
If there is not a defined B-state, then parameters from the A-state are applied,
hence no transformation. Another approach is to hack the topology such that the
ions you want to decouple are all in the same [moleculetype].
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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