Hi Justin, 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.
Thanks again! Yun Yun Shi wrote: > 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? > Check your units and the column headings of Table 7. Plugging in 9.85 as the energy will give you a wildly inflated result. The C12 parameters listed are actually square roots and listed as 10^-3. I think you will find the resulting energies and forces are vastly smaller for a simple interaction between two atoms. > 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? > There is no need to update the neighbor list every single step. Typically, water is the fastest-diffusing molecule in the system, but it will generally not have a dramatic displacement on the scale of 10 fs or so. > 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? > PME is substantially more accurate. Using it also requires rlist=rcoulomb, so the exact details of the Gromos96 derivation may be somewhat outdated. Typical settings for Gromos96 would be something like: rlist = 0.9 rcoulomb = 0.9 rvdw = 1.4 nstlist = 5 coulombtype = PME Note that the value of rcoulomb and rlist can vary a bit as a consequence of PME. -Justin > Thanks a lot, > > Yun Shi > > > On 04/08/11, "Justin A. Lemkul" <jalem...@vt.edu > <mailto:jalem...@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 > interactions. > > > > > > 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. > > Mark > > > > > > > > >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? > > > > > > > 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 > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 > <tel:%28540%29%20231-9080> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ============================== ========== > > -- > > gmx-users mailing list gmx-users@gromacs.org > <mailto:gmx-users@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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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