[gmx-developers] soft-core potential

Fan Hao F.Hao at chem.rug.nl
Mon Jul 29 13:24:23 CEST 2002

Hi, all:
	I have a problem when I tried to use soft core potential in my MD
simulation. I don't want to do free energy perturbation but only want to
have soft core interaction. So I set state A to be the same as state B, I
mean, all the atom type, charge and mass are the same for both A and B.
However I found I can not have soft core interaction in this way. I am not
sure but I think it is because gmx check the md->bPerturbed[] in
simulation. I just wonder whether it is good to set md->bPerturbed[*] to
be TRUE to get the soft core. Any advice are appreciated!  
My system :	
	protein and spc water while the hydrogens in protein
are all dummies.
My parameter :
	free-energy              = yes
	init-lambda              = 0.5
	delta-lambda             = 0
	sc-alpha                 = 1.51
	sc-sigma                 = 0.3 

Best regards

Yours sincerely

Hao Fan :-)

Drs. Hao Fan                            email F.Hao at chem.rug.nl
Lab. of Biophysical Chemistry
University of Groningen
Nijenborgh 4                            9747 AG GRONINGEN
The Netherlands

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