[gmx-users] The pull rate of AFM

Thomas Schlesier schlesi at uni-mainz.de
Mon Aug 10 16:02:08 CEST 2009

Hi, in GROMACS 3.3.x you must normalize the afm_dir1 vector by hand (or otherway around: afm_dir1 should be normalized).
Your vector is about 2.2 long -> so your pull-rate is 0.0022 -> and you see a much longer pulling distance (4nm against 2nm).
In GROMACS 4.0.x the vector is normalized automatically.
Hope this helps.


Dear all, 

   First, how to search the mailing list in the new website? I didn't find the button.
   Because I failed to search the mailing list, I post the following question that may be discussed before. I used the pull code for simulation, here is my pull.ppa file:

verbose            = no 
skip steps         = 10
runtype            = afm
group_1            = G_pull
reference_group    = Ref
reftype            = com
pull_dim            = Y Y Y

afm_rate1                = 0.001 ;nm/ps
; Force constants in kJ/(mol*nm2)
afm_k1                   = 4184
; Directions
afm_dir1                 = 0.324761469	1.699368642	-1.350340856
afm_init1                = -0.461723435	0.925478896	-0.835222495

	My simulation time is 2 ns with a time step 2fs. If the unit of pull rate is nm/ps, the dummy atom should move 2 nm. However, I found that the dummy atom moved 4 nm! So, the unit of pull rate is (dt*nm)/(1fs*ps)? Right? I used Gromacs-3.3.1 for the simulation. Thanks!

Best regards,

Dechang Li, Ph.D Candidate
Department of Engineering Mechanics
Tsinghua University
Beijing 100084
P.R. China 

Tel:   +86-10-62773574(O) 
Email: lidc02 at mails.tsinghua.edu.cn


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