[gmx-users] CG of molecule in water

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 25 12:15:29 CEST 2018


Such transferability should not be assumed. If the two components had also
been paramterized for e.g. density of the mixture then you would likely not
have chosen the same end point of optimal parameter values. The
combinations might work well enough, but that needs to be shown.


On Wed, Apr 25, 2018 at 7:20 AM Alex <alexanderwien2k at gmail.com> wrote:

> Dear all,
> Just suppose the system of course-grained (CG) study is a molecule in
> water. The bonded and nonbonded CG parameters for molecule are available in
> the format of table_b1.xvg, table_b2.xvg, table_a1.xvg, table_A_A.xvg,
> table_A_B.xvg ... . The parametrization has been performed in the pure
> molecule phase without water. In the another side the water CG parameters
> are available also in the table_W.xvg ... format parametrized in the pure
> water phase.
> Now, for the CG study of molecule in water, I was wondering if I can just
> mix the molecule and water and use those table which have been parametrized
> separately in pure phases, and just let the combination rule governs on the
> interaction of molecule and water, similar to the atomistic simulation?
> Or I have to parametrize them (obtain the tables for molecule and water) in
> the presence of each others?
> Thanks.
> Regards,
> Alex
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