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<P><FONT SIZE=2>Hi<BR>
I am trying to use the pull code of gromacs (version 4.5.5) to constrain the com of a number of groups (labelled CIT, CIT1, CIT2...) to a reference group (labelled GOLD). This is the segment of the .mdp file I have used:<BR>
<BR>
;CoM pull calculations<BR>
pull = constraint<BR>
pull_geometry = distance<BR>
pull_dim = N N Y<BR>
pull_constr_tol = 1e-6<BR>
; add COM distance of starting config to pull_init<BR>
pull_start = yes<BR>
;frequency for writing COMS of all pull group<BR>
pull_nstxout = 10<BR>
;frequency for writing force of all pull group<BR>
pull_nstfout = 10<BR>
pull_ngroups = 12<BR>
;name of reference group<BR>
pull_group0 = GOLD<BR>
pull_group1 = CIT<BR>
pull_group2 = CIT1<BR>
pull_group3 = CIT2<BR>
pull_group4 = CIT3<BR>
pull_group5 = CIT4<BR>
pull_group6 = CIT5<BR>
pull_group7 = CIT6<BR>
pull_group8 = CIT7<BR>
pull_group9 = CIT8<BR>
pull_group10 = CIT9<BR>
pull_group11 = CIT10<BR>
pull_group12 = CIT11<BR>
;reference distance at t=0 (nm)<BR>
pull_rate1 = 0<BR>
pull_rate2 = 0<BR>
pull_rate3 = 0<BR>
pull_rate4 = 0<BR>
pull_rate5 = 0<BR>
pull_rate6 = 0<BR>
pull_rate7 = 0<BR>
pull_rate8 = 0<BR>
pull_rate9 = 0<BR>
pull_rate10 = 0<BR>
pull_rate11 = 0<BR>
pull_rate12 = 0<BR>
<BR>
However, when I look at the output only the first pull group (CIT) is being restrained at a constant com height from GOLD. The others move away.<BR>
<BR>
output from pullx.xvg:<BR>
0.0400 0.717773 0.984186 0.977682 0.979256 0.975962 0.978739 0.974255 0.969942 0.97706 0.987668 1.00157 0.979894 0.982414<BR>
0.0500 0.717776 0.985442 0.977141 0.979625 0.976002 0.978158 0.973563 0.968578 0.97746 0.989067 1.00363 0.980026 0.983273<BR>
0.0600 0.717776 0.986709 0.976605 0.980068 0.976034 0.977671 0.973037 0.967893 0.977855 0.990371 1.00531 0.980148 0.984034<BR>
0.0700 0.717776 0.987965 0.976222 0.98048 0.976129 0.977231 0.972626 0.967535 0.978239 0.991569 1.00703 0.980298 0.984731<BR>
0.0800 0.717776 0.989129 0.976023 0.980946 0.976285 0.976717 0.972257 0.967184 0.978667 0.99272 1.0089 0.980504 0.985445<BR>
0.0900 0.717776 0.990186 0.97597 0.98157 0.976445 0.976252 0.971888 0.966841 0.97909 0.993944 1.01091 0.980784 0.986181<BR>
0.1000 0.717776 0.991179 0.976024 0.982275 0.9766 0.975847 0.971445 0.966549 0.979437 0.995328 1.01311 0.98115 0.986935<BR>
0.1100 0.717776 0.992167 0.976165 0.982984 0.976787 0.975344 0.970858 0.966275 0.979715 0.996957 1.01556 0.981619 0.987732<BR>
<BR>
I was wondering what I have done wrong in the input .mdp file. >From looking at the manual, I can't work it out since I think I have set it up as shown.<BR>
<BR>
Thanks in advance<BR>
Louise<BR>
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