[gmx-users] setting vdw cutoff with specific force-filed?

Yun Shi yunshi09 at gmail.com
Thu Aug 4 18:20:58 CEST 2011

Hi Justin and Mark,

Thank you very much for the reply.

I was using table 7 (Normal van der Waals Parameters) to calculate
non-bonded vdw interactions that are not between third neighbors, such as
CH1 carbons between different chains in a biomolecular system. Anything
wrong here?

I understand that it is the force that dictates the MD evolution, and I
calculated in this case as F = 12 * 9.85^2 / 1.5^13 = 5.98 kJ/mol/nm for the
repulsion term. The force from different directions on a atom in a
homogeneous system would cancel each other to some extend, but what about
the energy arises from this interaction? Would this considerably affect the
calculation of, say, binding energy of a ligand to a receptor from
thermodynamic integration or pulling simulation?

Besides, the GROMOS 53a6 paper used triple range scheme for calculations of
nonbonded interactions, and I guess it was rlist = 0.8 nm while rvdw =
rcoulomb = 1.4 nm. So is this considered to be accurate enough in
calculating free enthalpies of solvation since we know the interactions
between 0.8 and 1.4 nm were calculated every 5 steps?

The paper also used reaction-field instead PME to account for long-range
electrostatic interactions. I heard some people argue that PME would be more
accurate and it seemed to be utilized more often even in gromacs tutorials.
So does this mean certain accuracy could be achieved by using triple range
scheme and reaction-field together because the errors they incur
respectively somehow cancel out each other?

Thanks a lot,

Yun Shi

On 04/08/11, "Justin A. Lemkul"  <jalemkul at vt.edu> wrote:
> Yun Shi wrote:
> >Hi all,
> >
> >I am working with GROMOS 53a6 ff in GROMACS 4.5, and I assume a
Lennard-Jones interaction function was used for short-range vdw
> >
> > From the reference paper /A Biomolecular Force Field Based on the Free
Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets
53A5 and 53A6/, I found that for example,
> >
> >when rvdw = 1.5nm, the repulsion term of the interaction between two CH1
type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 / (1.5^12) =
0.747786 kJ/mol. So I wonder if this value is considered to be small enough
to be ignored.

You should pay attention to the column headings in table 7 so that you can
compute the contribution correctly. However, the magnitude of the energy of
any particular interaction is not really of any concern. The evolution of
the system depends on the *forces*, and it is likely that the sum of the
forces on any atom from all its repulsion interactions from atoms that are
(say) 1.4nm to 1.5nm away is very close to zero, except in highly
non-homogeneous spatial distributions of particles. In any case, the sum of
that contribution will be much smaller than the other contributions.


> >
> >In addition, it seems not until 5 nm does the dispersion term become
larger than the repulsion term in this case, so would turning on Dispersion
Correction between, say 1.5 to 5 nm introduce more errors than turning it
> >
> You should use the cutoff described the authors of the force field, in
this case rvdw=1.4.  Unless you can demonstrate that by using a different
value you can achieve superior results, stick with the specifics of
parameterization.  I have never seen ill effects of setting rvdw=1.4 and
using dispersion correction with this force field.
> -Justin
> --
> ==============================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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