[gmx-users] input file in umbrella sampling

Hwankyu Lee leehk at umich.edu
Tue Nov 29 18:16:04 CET 2005

Dear gmx-users,

1) I would like to do umbrella sampling with the distance restraint 
between COMs of two helix peptides, which allows the peptides to 
rotate. Does my ppa file looks fine?  KID5 peptide are reference group, 
and the distance between KID5 and KID6 is approximately 1nm in initial 

My ppa file is below.
verbose = no
runtype = umbrella
group_1 = KID6
reference_group = KID5
reftype = com
k1 = 1000

2) I may have to adjust k1 value because it does not have to be too 
stiff or loose, but I wonder if there is a range of reasonable k1 value 
in this case.

Thanks for your help in advance.


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