Hi Justin,<br><br>I got it now. During the 10fs, even water molecules with a speed of 500 m/s only have a 0.005 nm displacement, which is far less than than 0.9 nm or 1.4 nm.<br><br>Thanks again!<br><br>Yun<br><br><br>Yun Shi wrote:<br>
> 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<br>
> non-bonded vdw interactions that are not between third neighbors, such<br>
> as CH1 carbons between different chains in a biomolecular system.<br>
> Anything wrong here?<br>
><br>
> I understand that it is the force that dictates the MD evolution, and I<br>
> calculated in this case as F = 12 * 9.85^2 / 1.5^13 = 5.98 kJ/mol/nm for<br>
> the repulsion term. The force from different directions on a atom in a<br>
> homogeneous system would cancel each other to some extend, but what<br>
> about the energy arises from this interaction? Would this considerably<br>
> affect the calculation of, say, binding energy of a ligand to a receptor<br>
> from thermodynamic integration or pulling simulation?<br>
><br>
<br>
Check your units and the column headings of Table 7. Plugging in 9.85 as the<br>
energy will give you a wildly inflated result. The C12 parameters listed are<br>
actually square roots and listed as 10^-3. I think you will find the resulting<br>
energies and forces are vastly smaller for a simple interaction between two atoms.<br>
<br>
> Besides, the GROMOS 53a6 paper used triple range scheme for calculations<br>
> of nonbonded interactions, and I guess it was rlist = 0.8 nm while rvdw<br>
> = rcoulomb = 1.4 nm. So is this considered to be accurate enough in<br>
> calculating free enthalpies of solvation since we know the interactions<br>
> between 0.8 and 1.4 nm were calculated every 5 steps?<br>
><br>
<br>
There is no need to update the neighbor list every single step. Typically,<br>
water is the fastest-diffusing molecule in the system, but it will generally not<br>
have a dramatic displacement on the scale of 10 fs or so.<br>
<br>
> The paper also used reaction-field instead PME to account for long-range<br>
> electrostatic interactions. I heard some people argue that PME would be<br>
> more accurate and it seemed to be utilized more often even in gromacs<br>
> tutorials. So does this mean certain accuracy could be achieved by using<br>
> triple range scheme and reaction-field together because the errors they<br>
> incur respectively somehow cancel out each other?<br>
><br>
<br>
PME is substantially more accurate. Using it also requires rlist=rcoulomb, so<br>
the exact details of the Gromos96 derivation may be somewhat outdated. Typical<br>
settings for Gromos96 would be something like:<br>
<br>
rlist = 0.9<br>
rcoulomb = 0.9<br>
rvdw = 1.4<br>
nstlist = 5<br>
coulombtype = PME<br>
<br>
Note that the value of rcoulomb and rlist can vary a bit as a consequence of PME.<br>
<br>
-Justin<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><br>
> <mailto:<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<br>
> Lennard-Jones interaction function was used for short-range vdw<br>
> interactions.<br>
> > ><br>
> > > From the reference paper /A Biomolecular Force Field Based on the<br>
> Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field<br>
> Parameter Sets 53A5 and 53A6/, I found that for example,<br>
> > ><br>
> > >when rvdw = 1.5nm, the repulsion term of the interaction between two<br>
> CH1 type atoms (C12ij = 9.85^2) can be calculated as 9.850*9.850 /<br>
> (1.5^12) = 0.747786 kJ/mol. So I wonder if this value is considered to<br>
> be small enough to be ignored.<br>
> ><br>
><br>
> You should pay attention to the column headings in table 7 so that you<br>
> can compute the contribution correctly. However, the magnitude of the<br>
> energy of any particular interaction is not really of any concern. The<br>
> evolution of the system depends on the *forces*, and it is likely that<br>
> the sum of the forces on any atom from all its repulsion interactions<br>
> from atoms that are (say) 1.4nm to 1.5nm away is very close to zero,<br>
> except in highly non-homogeneous spatial distributions of particles. In<br>
> any case, the sum of that contribution will be much smaller than the<br>
> other contributions.<br>
><br>
> Mark<br>
><br>
> ><br>
> > ><br>
> > >In addition, it seems not until 5 nm does the dispersion term become<br>
> larger than the repulsion term in this case, so would turning on<br>
> Dispersion Correction between, say 1.5 to 5 nm introduce more errors<br>
> than turning it off?<br>
> > ><br>
> ><br>
> > You should use the cutoff described the authors of the force field,<br>
> in this case rvdw=1.4. Unless you can demonstrate that by using a<br>
> different value you can achieve superior results, stick with the<br>
> specifics of parameterization. I have never seen ill effects of setting<br>
> rvdw=1.4 and using dispersion correction with this force field.<br>
> ><br>
> > -Justin<br>
> ><br>
> > --<br>
> > ==============================<br>
> ==========<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="http://vt.edu/" target="_blank">http://vt.edu/</a>> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
> <tel:%28540%29%20231-9080><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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<br>
--<br>
========================================<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></div><br>