[gmx-users] AFM pulling - how to get force-extension curves

Marc Baaden baaden at smplinux.de
Wed Jan 23 19:58:42 CET 2002

tieleman at ucalgary.ca said:
>> As reference position it takes the position at t=0 of the group you're
>>  pulling. The way it's done in the distribution, it doesn't do (v*T)
>> but  instead adds the displacement every step.

OK. That's about what I guessed, but you still (in principle) have
cst. + v*T
with cst.=reference pos.,v=displacement, T=stepnumber

The value is actually given in the logfile
Initial coordinates center of mass:   99.712    0.048   99.589

but strangely enough is not the value you get when writing out
the coordinates: -0.411255
which confuses me.

>> Try running in double precision and see if your output
>> makes more sense.

Done that. Doesn't make (much) more sense :((
I stil cannot reproduce the force !

>> I don't remember for sure but if you use verbose in
>> the pulll parameter  file it might tell you the position of the string
>> too. 

Yes it does indeed, but the precision is too low:
0:0: f:   0.026 s:  99.589
(add 0.00005 to it, and you see what I mean)

Is it possible to increase the precision for this output ?

Thanks for all replies,


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
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