>Thank you so much for your explanation. I am just guessing in the last >statement you meant *inter* molecular!
Yes. INTERmolecular, between chemically nonbonded particles. >> >> Formally, you can kill this energy by going to the main topology file >> (like ffgmx.itp) and setting FudgeLJ term to zero, although I think >> that you don't actually want to do so. LJ-14 is the energy between the >> atoms belonging to the SAME molecule, so if you consider e.g. heat of >> vaporization, cohesive energy density, internal energy (U), you can >> just ignore this term. >> >> If I recollect correctly, nexcl and 1-4 interactions work >> independently. "nexcl" requests to treat the atoms as if they belong >> to separate molecules provided that these two atoms are separated by >> more than a specified number of chemical bonds. 1-4 interactions only >> treat 1-4 atoms using a scaling factor from FudgeLJ (above). >> >> When calculating some intramolecular property, you usually need to use >> only the following terms > > I assume you mean intermolecular here? > >> LJ-(SR) Disper.-corr. Coulomb-(SR) Coul.-recip. >> > > There may be others, depending on the way in which the .mdp file was set, > including LR terms for both LJ and Coulomb. The PME term is not trivially > decomposed, but that's been discussed to death in previous messages. There > may be other terms if PME was not used. Of course. These four are just an example for the most traditional setup for periodic boxes with electrostatics. >> >> >> >> >> On Fri, Aug 26, 2011 at 3:12 PM, Juliette N. <joojoojo...@gmail.com> >> wrote: >>> >>> On 26 August 2011 13:25, Dr. Vitaly V. Chaban <vvcha...@gmail.com> wrote: >>>>>> >>>>>> . Now it is clear that >>>>>> the sum of [ LJ-14 + LJ (SR) ] give the actual non bonded potentials. >>>>>> Thank >>>>>> you so much. >>>> >>>> The answer actually depends on what you call "nonbonded potential". If >>>> you want to calculate e.g. the interaction energy between two >>>> molecules, then you should NOT include this term. >>> >>> Thank you for you reply. I am actually interested in interaction energies >>> (cohesive energy between particles which is related to enthalpy of >>> vaporization) and noticed that inclusion of this term results in far less >>> accurate results. The net energy is of repulsion type and adding a >>> positive >>> term ( LJ-1-4) makes my results inaccurate. I am already using nexcl = 3 >>> in >>> the topology which means 1-5, 1-6 neighbors are accounted for. But still >>> LJ >>> -1-4 is appearing. So far I have been ignoring this term (energy value) >>> in >>> my calculations, but my concern is that by just neglecting this energy >>> term >>> (value) I am not ignoring the actual effect of a potential term on the >>> physics of the system. Is there any way to switch off this term? >>> >>> Thanks, >>>> >>>> -- >>>> Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. >>>> Univ. Rochester, Rochester, New York 14627-0216 >>>> THE UNITED STATES OF AMERICA >>>> -- >>>> gmx-users mailing list 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. >>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> >>> -- >>> Thanks, >>> J. N. >>> >>> > > -- > ======================================== > > 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 > > ======================================== > -- Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept. Univ. Rochester, Rochester, New York 14627-0216 THE UNITED STATES OF AMERICA -- gmx-users mailing list 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. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
