Liu Shiyong wrote:
Hi, Mark,
I tried your suggestion.
+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.pdb
+ editconf -f a6.pdb -o a6.gro -d 20.0
+ make_ndx -f a6.pdb -o a6.ndx
+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
title = b
cpp = /usr/bin/cpp
integrator = cg
dt = 0.002 ; ps !
nsteps = 1
rlist = 0.55
nstlist = 0
vdwtype = Cut-off
rvdw = 0.6
coulombtype = Cut-off
epsilon_r = 2
rcoulomb = 0.6
energy_grps = chAANDB_&_!H* chC_&_!H*
Here you're defining two energy groups. GROMACS calculates non-bonded
interactions by looping over all charge groups within an energy group.
Thus, as the error message says, you have an inconsistent set of these
groups. It seems to me no purpose could be served by such energy groups.
Force fields are not made to be decomposable in any such fashion.
Mark
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