[gmx-users] Re: Problem in AFM pulling, direction and output?

clark clarkzhy at tom.com
Tue Nov 28 01:52:30 CET 2006

Dear all:
       Thank you very much,Emily Walton!
       Thank for all here!

My pull.ppa file is shown in the following:
verbose		= no
runtype		= afm
ngroups		= 1
group_1		= Lig
reference_group   = Protein 
reftype		= com 
pulldim		= Y Y Y
afm_rate1	         = 0.001 
afm_k1		  	 = 500 
afm_dir1	         = 0.588 0.428 -0.686
afm_init1	         = 0.788 0.204 0.534

and the output about AFM in the *.log file is :
Initializing pull groups. Inv. mass of group 1: 0.024950
Initial coordinates center of mass:    3.966    3.338    3.648
Initializing reference group. Inv. mass: 0.000132
Initial coordinates center of mass:    3.162    3.127    3.097
Initial distance of group 1:    0.998

Pull rate: 1.000000e-03 nm/ns. Force constant: 5.000000e+02 kJ/(mol nm)
Pull direction:    0.806    0.212    0.552

then ,you could find the difference of direction in two files. would you please tell me what makes these different?

By the way, Gromacs-3.3.1 is run in my PC-linux machines.

There is another problem. I couldn't find the "force" information in my pull.pdo. There are only the "coordinates" information in this file. Do I need to calculate the "force" value in every step by myself? 

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