[gmx-users] AFM pulling options

alicia at biof.ufrj.br alicia at biof.ufrj.br
Wed Jul 31 23:39:00 CEST 2002

we're having some problems with the AFM pulling option: we're trying to 
calculate AFM interacting forces between two reference groups and we found out 
that the output file .pdo looks all like this:
0:0: f:   0.000 s:   2.022
1:0: f:   0.000 s:   2.022
2:0: f:   0.000 s:   2.022
3:0: f:   0.000 s:   2.022
4:0: f:   0.000 s:   2.022
5:0: f:  -0.000 s:   2.022
6:0: f:  -0.000 s:   2.022
7:0: f:  -0.000 s:   2.022, etc
independently of the pulling rate parameters (even when trying higher pulling 
Here there is a description of the input file pull.ppa which we believe it's 
; Temperature, friction coefficient (amu/ps) and random seed = 
verbose = yes
runtype = afm
group_1 = 1cag_AN  
reference_group = 1cag_BC    
reftype = com
reflag = 1
direction = 1.0 0.0 0.0
reverse = from_reference
update = 1
pullrate = 0.00002 
forceconstant = 500.

Questions: 1) Are we doing the right thing?
2) Is the output file .pdo reliable, and if it is not, how do we get the force 
information we want? We allready tried to get this info using the g_traj 
program with the options:
g_traj -s pull.tpr -f pull.trr -com -of -n pull.ndx
but we suppose that it's calculating something different, since we are not 
asked for the reference group; only the group_1 is required. Is this option 
calculating the total interaction force acting on the center of mass of this 
last group due to the rest of the system?
Thanks in advance,

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