Dear Justin, Thanks for your reply and Sorry for asking naive questions...
1- I am looking at all possible interaction energies between components A and B. that is A-A AB and BB. So interaction between single chains is not what I want. With this I think my initial approach was right. That is putting all atoms of 3 A chains under [A] and the same all solvent atoms under [B] and setting A and B as energy groups in mdp. Am I right? 2- One more thing bout question 3: I am passing on index.ndx to mdrun command. with the index file I talked about I am getting the follwoing for AA AB and BB: LJ SR, LJ 1-4 coulomb SR and 1-4. (i.e 12 energy terms). I think you say I need rerun since you assumed I did not pass it onto mdrun. right? 3- to get intermolecular interaction energies say for AA I need to add up LJ SR+coulomb SR? say +123-50=73 ? or just take absolute values : 123+50=173 ? Thanks, > > Nick wrote: > >> Dear experts, >> >> 1- I am trying to get interaction energies between solute (3 chains A) and >> solvent 50 molecules B. In the index file I created two groups: one for all >> atoms of [A] and and [B] for all solvent molecules. and by setting A and B >> as energy groups in mdp file I am getting break down as A-A, A-B and B-B >> with g_energy. >> >> I am a little confused as I dont know if I need to create different groups >> for my solute to get interaction energies A-A, A-B and B-B. I mean do I need >> to have [A1] for solute chain 1 ...[A3] for chain 3? >> >> > If you want a breakdown of per-chain energetics, then yes, specify each > chain as a group. The programs will only do what you tell them, nothing > more, nothing less. > > > > and then sent A1, A2, A3 in mdp file and run g_energy? if I need to >> specify different chains, then to get say A-A should I average over all >> possible A1-A2, A1A3, A2-A3, A1-B, A2,B...? I am really confused .. >> >> > Theoretically, the short-range terms should sum, not average. > > > 2- I know it is naive question but What does A1-A1 mean? How can one chain >> interact with itself? >> >> > Without knowing what the chain is, no one can answer this. Generally, any > atoms that are within the short-range cutoff and further away than nrexcl > bonds contribute to short-range interactions. Long-range interactions > (i.e., PME terms) happen too, but you can't decompose that term with > energygrps. > > > 3- Do I need to use mdrun - rerun option to get beakdown or just g_energy >> gives what I need? >> >> > You need to -rerun. g_energy does not take an index file, and it only > analyzes existing groups, it cannot derive new ones. > > -Justin > > > Thanks for your help >> Paniz >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
