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<DIV><FONT size=4>Hi David:</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>I am sure there is no constraints.
<%--AID_SENDTO_BEGIN--%>David van der Spoel<%--AID_SENDTO_END--%></FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>In the mdp file:</FONT></DIV>
<DIV><FONT size=4>; OPTIONS FOR BONDS
<BR>constraints
= none<BR>; Type of constraint
algorithm<BR>constraint-algorithm = Lincs<BR>; Do not
constrain the start
configuration<BR>unconstrained-start =
yes</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>and i use the pull code to simulate the same process.
</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT
size=4>runtype
= afm</FONT></DIV>
<DIV><FONT
size=4>group_1
= a_1</FONT></DIV>
<DIV><FONT
size=4>reference_group =
a_2</FONT></DIV>
<DIV><FONT
size=4>afm_rate1
= 0.0001</FONT></DIV>
<DIV><FONT
size=4>afm_dir1
= 0.0 0.0 1.0</FONT></DIV>
<DIV><FONT
size=4>afm_k1
= 10000</FONT></DIV>
<DIV><FONT
size=4>afm_init1
= 0.0 0.0 0.142</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>The initial gro:</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>1CNT C1
1 1.500 1.500 <FONT
color=#ff0000>1.571</FONT> -0.0488 0.2871
0.0382<BR>1CNT C2 2
1.500 1.500 1.429 0.2162 0.1612
0.0378</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>The result gro:</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>1CNT C1
1 1.500 1.501 <FONT
color=#ff0000>2.561</FONT> 0.0000 0.0000
0.0001<BR>1CNT C2 2
1.500 1.500 1.429 0.0000 0.0000
-0.0001</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>Then I calculate the pull force F(add)= k1*(rate*T-Rij) =10000
*(0.0001*10000-(2.561-1.571))=100pN. Is it right?</FONT></DIV>
<DIV><FONT size=4>The bond force
F(bon)=kb*(Rij)=100*(2.561-1.571)=99pN</FONT></DIV>
<DIV><FONT size=4>But at this moment the a_1 atom is still moving!!
</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>why?</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>Thank you .</FONT></DIV>
<DIV><FONT size=4></FONT> </DIV>
<DIV><FONT size=4>Qi Wenpeng</FONT></DIV></BODY></HTML>