xiao shijun wrote:
Thanks for Mark's fast reply, and It really works.
Then, I have another qusetion about the manual: It seems that the
exclusion just excludes the nonbond potential of LJ interaction, but
Buckingham. If we want to turn off all VDW interaction between some
atoms, the energy monitor group is a nice choice. I have no idea if I
got it right.
And, we can't use LJ and Buckingham in a same system. Unfortunately,
I met a force-field that most of the nonbond interactions were described
by Buckingham, but LJ only for Ow-Ow among water. I chose nbfunct=2 in
[defaults] section,and nbfunct=1 in [nonbond_params] for Ow-Ow. As a
result, a error message read: *Trying to add LJ (SR) while the default
nonbond type is Buck.ham (SR). *I don't know whether it could be
settled in gromacs.
AFAIK, you could only do this with tabulated functions. You can supply a
normal Buckingham table (generated with mdrun -debug?) with vdwtype =
User, and water-water tables separately with energygrp_table. This will
be slower than any native implementation, but still decent.
See manual section 6.7 and 7.3.12. I'd strongly suggest starting with
peptide-in-water test case that was mixing different degrees of LJ
parameters so that you're confident of your use of the table and
energygrp_table mechanisms, before trying to mix Buckingham and LJ in
the way you're describing.
Mark
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