<div>Hello GMX user,</div>
<div> </div>
<div>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:</div>
<div><br clear="all">ngroups = 1<br>group_1 = UNK<br>reference_group = STACK<br>reftype = com<br>reflag = 1<br>pulldim = Y Y Y</div>
<div>afm_rate1 = 0.002<br>afm_k1 = 1673<br>afm_dir1 = <span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 华文新魏; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA">X3-X1, Y3-Y1, Z3-Z1</span></div>
<div><span lang="EN-US" style="FONT-SIZE: 12pt; FONT-FAMILY: 'Times New Roman'; mso-fareast-font-family: 华文新魏; mso-font-kerning: 1.0pt; mso-ansi-language: EN-US; mso-fareast-language: ZH-CN; mso-bidi-language: AR-SA"></span>afm_init1 = <font face="Times New Roman" size="3">0.0, 0.0 ,0.0</font></div>
<div><font face="Times New Roman" size="3"></font> </div>
<div><font face="Times New Roman" size="3">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?</font></div>
<div> </div>
<div>Thank you very much!</div>
<div>Huifang</div>
<div><br><br>-- <br>Huifang Liu (Ph.D. Student)<br>School of Pharmacy<br>Fudan University<br><br>138 Yi Xue Yuan Rd. Tel: (86-21)54237419 (O)<br>Shanghai, China, 200032 Cell phone: +86-13764669357<br>E-mail: <a href="mailto:huifangliu1985@gmail.com">huifangliu1985@gmail.com</a> Fax: (86-21)54237264<br>
</div>