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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