[gmx-users] Implicit solvent simulation of protein folding

[tsikosek]

UPDATE:

I found these parameters to work:
http://comments.gmane.org/gmane.science.biology.gromacs.user/52770

Now I have a follow up question.

It seems that at 300K my unfolded protein chain quickly collapses into some
random conformation and more or less stays that way without much
conformational sampling, especially when I compare it to an explicit solvent
simulation at the same temperature. 

I only get decent sampling above 400K.

Can anyone explain why that might be? Could it have to do with the implicit
solvent parameters I'm using ?

The parameters are:
implicit_solvent    =  GBSA
gb_algorithm        =  Still
nstgbradii          =  1
rgbradii            =  0
gb_epsilon_solvent  =  80
sa_algorithm        =  Ace-approximation
sa_surface_tension  = -1

Thanks in advance for any help!

Tobias



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