[gmx-users] problems with pulling direction and the initial spring position

huifang liu huifangliu1985 at gmail.com
Tue Mar 10 09:23:14 CET 2009

Hello GMX user,

I want to pull  a compound named UNK (whose initial center of mass is X1,
Y1, Z1) through a nanotube named STACK(whose center of mass is X2, Y2, Z2).
The final position of  UNK is supposed to be around X3, Y3, Z3. I used the
pull.ppa file as follows:

ngroups                  = 1
group_1                  = UNK
reference_group          = STACK
reftype                  = com
reflag                   = 1
pulldim                  = Y Y Y
afm_rate1                = 0.002
afm_k1                   = 1673
afm_dir1                 = X3-X1, Y3-Y1, Z3-Z1
afm_init1                = 0.0, 0.0 ,0.0

What make me confused is that when the UNK is pulled to the center of mass
of the channel (nanotube), it begins to fluctuate around the center and
doesn't go through the channel. Why could the UNK not be pulled forwards?
How can i solve this problem? In addtion, do i use the correct options of
afm_dir1 and afm_init1?

Thank you very much!

Huifang Liu (Ph.D. Student)
School of Pharmacy
Fudan University

138 Yi Xue Yuan Rd.          Tel: (86-21)54237419 (O)
Shanghai, China, 200032     Cell phone: +86-13764669357
E-mail: huifangliu1985 at gmail.com Fax: (86-21)54237264
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