[gmx-users] Free energy profiles with Pull code : dimer/dimer interactions

CROUZY Serge 119222 serge.crouzy at cea.fr
Wed Nov 2 17:24:48 CET 2016

Dear gromacs users

In previous mail on the list Justin argued about free energy calculations with Pull code that:
"For general
protein-ligand complexes, it is *NOT* appropriate to assume 
one-dimensional pulling or applying position restraints to the 
protein.  Our paper (from which the tutorial was derived) describes 
the somewhat unique case we were dealing with. "

 In my case, I'm calculating the profile for dimer dissociation in a 
 tetramer of proteins pulling on 1 dimer in direction X (because the 
tetramer is oriented in a such a way that X is the principal axis) 
while the other dimer is harmonically restrained (BB atoms only) 
I don't see how this could be done differently; although I'm hoping that 
 the free energy will result from the sole force between dimer/dimer 
 atoms: the restraint on one dimer should not affect the result .. As 
 long as they do not prevent the fluctuations (breathing) necessary for an almost reversible extraction of 
one dimer  from the tetramer. Is there a paper describing the possible effect of 
these restraints on the profile ?  (I suppose if one dimer is 
 completely fixed, the energy barrier for extraction will increase 
 dramatically because its residues won't be allowed to adjust while the 
 partner dimer is pulled out)

Thanks for your input

Serge Crouzy PhD HDR
Groupe de Modélisation et Chimie Théorique
Laboratoire de Chimie et Biologie des Métaux 
Institut de Biosciences et Biotechnologies de Grenoble
CEA Grenoble  UMR  CEA/CNRS/UJF 5249
17, rue des martyrs
38054 Grenoble Cedex 9
Bat. K  pièce 110   
Tel (33)0438782963
Fax (33)0438785487

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