[gmx-users] Re: Re: Size of perturbed groups in FEP

Bruce Milne bfmilne at ff.up.pt
Fri Jan 13 13:27:06 CET 2006


Thanks everyone for your answers. I think I understand the point about 
correlation times possible being long for FEP of D-/L-amino acids in 
small peptides (these would be octapeptides) as there are significant 
intra-molecular interactions with the side-chains that influence the 
conformation of the molecule - if the system is perturbed from D to L 
configuration a conformational change would be expected and this would 
have to be allowed to stabilise into a new conformational potential well.

Also, when perturbing large bulky groups, more time would be needed for 
rearrangement of solvent as the group's interactions with it 
grow/shrink. So because of both of these points a long simulation with 
slow rate of change of the perturbed group(s) would be best - am I right?

Thanks again,


Dr. Bruce F. Milne PhD
Faculdade de Farmácia
Universidade do Porto
Rua Aníbal Cunha - 164

email: bfmilne at ff.up.pt
CEQOFFUP: http://www.ff.up.pt/ceqoffup/ceqoffup.html
Faculdade de Farmácia: http://sigarra.up.pt/ffup/web_page.inicial

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