[gmx-users] The pull rate of AFM

[Thomas Schlesier]

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.
Thomas


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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,
2009-8-8


========================================= 
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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