[gmx-users] AFM pulling - how to get force-extension curves
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
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
mailto:baaden at smplinux.de - ICQ# 11466242 - http://www.marc-baaden.de
FAX/Voice +49 697912 39550 - Tel: +44 1865 275380 or +33 609 843217
More information about the gromacs.org_gmx-users