[gmx-users] energy groups

[Mark Abraham]

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