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<div>Just read your other responses, didnt know it would overide with vector set, but if it doesnt work try the _dim</div>
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<div>Stephan</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 29. Juli 2013 um 20:42 Uhr<br/>
<b>Von:</b> kim2811 <kmanibog@iastate.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> [gmx-users] constant force pulling</div>
<div name="quoted-content">Hi,<br/>
<br/>
I am trying to pull/separate a protein dimer by applying constant force in<br/>
my SMD. The dimer has dimension 9 x 8 x 5 nm^3, and I'm trying to pull in<br/>
the y-direction so I have set the box as 12 x 40 x 8 nm^3. I have also set<br/>
my simulation to run for 5 ns. However, after only 251 ps, I got this fatal<br/>
error:<br/>
<br/>
Distance of pull group 1 (3.958423 nm) is larger than 0.49 times the box<br/>
size (16.314939)<br/>
<br/>
Can somebody please interpret this error? When I checked the trajectory, the<br/>
protein seems to be inside the box or at least the COM of the dimer is near<br/>
the center of the box, so the protein approaching near the boundary can't be<br/>
the reason for this error. If it can help to clarify, here's my pull code:<br/>
<br/>
; Pull code<br/>
pull = constant_force<br/>
pull_geometry = direction ; pull in the direction of pull code<br/>
pull_dim = Y Y Y<br/>
pull_start = yes ; define initial COM distance > 0<br/>
pull_ngroups = 1<br/>
pull_group0 = chain_A ; C-terminal of Protein 1<br/>
pull_group1 = chain_B ; C-terminal of Protein 2<br/>
pull_k1 = -500 ; kJ mol^-1 nm^-1<br/>
pull_vec1 = 0 1 0<br/>
<br/>
Thank you.<br/>
<br/>
<br/>
<br/>
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