[gmx-users] Alchemical transformation position restrains for B state and citing literature for H-RETI

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Thu Aug 3 08:37:34 CEST 2017

Dear all,

I have two questions concerning MD TI free energy calculations for 
alchemical transfromations:

1) (For some reasons) I want to restrain the backbone of my protein 
during TI. However, I do not know to correctly generate position 
restrains for the mutated B-state. 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?

2) I am using replica exchange ( -replex in the mdrun) during the free 
energy thermodynamic integration MD simulation (H-RETI). Can someone 
tell me the literature I should cite when I apply this?

All the best and thank you very much in advance


*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de

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