Hi Justin and Mark,<br><br>Thank you very much for the reply.<br><br>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?<br>
<br>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?<br>
<br>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?<br>
<br>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?<br>
<br>Thanks a lot,<br><br>Yun Shi<br><br><br>On 04/08/11, "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
><br>
><br>
> Yun Shi wrote:<br>
> >Hi all,<br>
> ><br>
> >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
interactions.<br>
> ><br>
> > 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,<br>
> ><br>
> >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.<br>
><br>
<br>
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.<br>
<br>
Mark<br>
<br>
><br>
> ><br>
> >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 off?<br>
> ><br>
><br>
> 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.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ==============================<div id=":31">==========<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
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