Hi 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:
;CoM pull calculations pull = constraint pull_geometry = distance pull_dim = N N Y pull_constr_tol = 1e-6 ; add COM distance of starting config to pull_init pull_start = yes ;frequency for writing COMS of all pull group pull_nstxout = 10 ;frequency for writing force of all pull group pull_nstfout = 10 pull_ngroups = 12 ;name of reference group pull_group0 = GOLD pull_group1 = CIT pull_group2 = CIT1 pull_group3 = CIT2 pull_group4 = CIT3 pull_group5 = CIT4 pull_group6 = CIT5 pull_group7 = CIT6 pull_group8 = CIT7 pull_group9 = CIT8 pull_group10 = CIT9 pull_group11 = CIT10 pull_group12 = CIT11 ;reference distance at t=0 (nm) pull_rate1 = 0 pull_rate2 = 0 pull_rate3 = 0 pull_rate4 = 0 pull_rate5 = 0 pull_rate6 = 0 pull_rate7 = 0 pull_rate8 = 0 pull_rate9 = 0 pull_rate10 = 0 pull_rate11 = 0 pull_rate12 = 0 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. output from pullx.xvg: 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 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 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 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 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 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 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 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 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. Thanks in advance Louise
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