Hi everyone; I am simulating a functionalized nanotube with (CH3) group .the nanotube atoms are uncharged and rigid but the atoms of (CH3) group are charged and flexible ,and are defined in the residue name of [atom] section of topology file with (CNT)and (FUNC) , Respectively. I have decided to freeze my CNT in all 3 directions. In fact , I have flexible group anchored to a frozen surface of CNT . thus , I used (energygrp_exl = CNT CNT , freezegrps = CNT , coulombtype = PME ) ,but I get the following warning upon running grompp.
Can not exclude the lattice coulomb energy between energy groups Please correct my .mdp file and add any requisite option in this p case. coulombtype = PME energygrps = CNT FUNC constraints = none energygrp_excl = CNT CNT freezegrps = CNT freezedim = Y Y Y Thank you
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