[gmx-users] Position restrains during alchemical transformation

[Hermann, Johannes]

Dear all,

I have a questions concerning MD free energy calculations using 
alchemical tranformation. I want to restrain the backbone of my protein 
which I mutate during TI. However, I do not know how to correctly 
generate position restrains. If I use the position restrain file, which 
I generated for the A state, following warning shows up:

WARNING 1 [file posre.itp, line 1470]:
   Some parameters for bonded interaction involving perturbed atoms are
   specified explicitly in state A, but not B - copying A to B

Can I ignore this warning, or do you have any suggestions for me?

All the best and thank you very much in advance

Johannes