[gmx-users] question regarding mutation from CH --> COH during free energy calculation
hyunjink at andrew.cmu.edu
Sat Jun 15 10:57:13 CEST 2013
I edit my topology file for mutating CH --> COH during free energy
Since one hydrogen atom attached to carbon disappears, while two O and H
atoms are appearing, I build topology file as follows:
8 opls_169 1 TEST O 3 -0.7 15.9994
opls_140 0.1 1.008
13 opls_140 1 TEST H6 4 0.1 1.008
opls_169 -0.7 15.9994
18 opls_155 1 TEST H10 5 0.455 1.008
DUM_155 0.0 1.008
25 DUM_155 1 TEST H15 7 0.000 1.008
opls_155 0.455 1.008
My questions are,
1. as you can see, I introduce a dummy atom in the A state and mutate H
--> O and dummy --> H. Is it correct?
2. if it is correct, then how should I build bonded parameters between H
(opls_140) and dummy (opls_155), since they do not exist.
I have searched for mailing list and tutorials, but I am still not clear
what is the correct way to edit topology file for my case.
I will appreciate that if you can suggest or help me regarding this issue.
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