Dear Mark, I will go for version 5.1.4 test whether the pairs_nb statement is valid. Thanks for you help and let me report to you soon.
Adolfo > Hi, > > When you're using a version of the software that's more than three years > old, and a bug was fixed less than two years ago, you need to get an > updated version :-) > > Once you do, your problem reduces to whether you can identify few enough > groups of atoms whose pairwise group-group interatomic interactions have > the same shape. They can use the same tables. Trying to use a different > table for eg each atom pair would run out of energy groups, and be an > utter > disaster for performance. > > Mark > > On Wed, 1 Mar 2017 10:18 <p...@ifpan.edu.pl> wrote: > >> Dear Mark, >> >> thanks for your comment regarding the pairs interaction. I did know >> about >> the tabulated choice for nb interaction, but the number of interaction >> will reach more than >200 pair. Even though, I go for the energy group >> description it will need a larger number of groups, as each entry will >> be >> assigned to one pair (i,j) with i and j index of particles. I have a >> Martini ff underneath, and sure I have several Martini types which >> reflect >> the amino acid character: (P)Polar, (A)Apolar, (I)Intermediate Polar and >> (C)Charge and in each different types(Qda,Nda,P1,P5,etc). If I use >> groups >> with P,A,I and C, then the issue will be, that I need to define >> interactions between four groups to describe specific interaction >> between >> CA atoms in each group. >> >> For instance, >> pair 1 and 34: involves groups (C)-(I) with types Qda and Nda >> pair 1 and 36: involves groups (C)-(I) with types Qda and Nda. >> >> the issue comes that one may need to use different sigmas which are >> defined by the distance between the pairs. >> >> The other pairs are also non-redundant due to atom indexes and different >> sigma parameters which are defined by the distance as well. >> >> Recenlty, I found another choice the [pairs_nb]. Guess you had a comment >> in the past regarding a deprecate directive see at >> >> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-May/097965.html >> >> Currently, I have problem to set it up. Look at a piece of my .itp file >> >> [pairs_nb ] >> 1 34 1 0.0 0.0 0.34962 0.00974 >> 1 36 1 0.0 0.0 0.29890 0.00712 >> >> with error: >> ******************************************************** >> Generated 0 of the 780 non-bonded parameter combinations >> case: 20 >> ------------------------------------------------------- >> Program grompp_mpi, VERSION 4.6.5 >> Source code file: >> /home/HDD3000/HOME_poma/poma/Software/gromacs-4.6.5/src/gmxlib/gmx_fatal.c, >> line: 597 >> >> Fatal error: >> Invalid case in switch statement, file >> /home/HDD3000/HOME_poma/poma/Software/gromacs-4.6.5/src/kernel/topio.c, >> line 1007 >> ******************************************************** >> >> initially I used [pairs] without the zeros entries for qi, qj and the >> last two terms are combination rules for V** and W** parameters. It >> worked >> as the system was in the minimum energy state (folded state). Now I >> started the simulation in the unfolded state and the distance between >> pairs may reach lengths longer than molecular cutoff. This is the reason >> why I do want to shift the pairs in context of non-bonded picture. Any >> insights will be highly appreciated, maybe I really miss the concept of >> the tabulate scheme & groups definition. >> >> best, >> >> Adolfo >> > Hi, >> > >> > Tabulated non-bonded potentials are possible (see manual), but >> currently >> > only implemented between pairs of energy groups, and only in the group >> > cut-off scheme. So by e.g. putting each type of particle in its own >> energy >> > group you can arrange for whatever inter-group interactions suit you. >> But >> > there's only a small number of groups possible, maybe 64 or 128? I >> forget. >> > >> > Mark >> > >> > On Tue, Feb 28, 2017 at 10:22 AM <p...@ifpan.edu.pl> wrote: >> > >> >> Hi, >> >> We had employed the pair potentials in unconventional way. They were >> >> used >> >> to describe nonbonded specific Lennard Jones (LJ) Potential between a >> >> pair >> >> of particles. Each pair has a different set of sigma's parameters, >> but >> >> just one epsilon. Although they are LJ potentials, they are >> considered >> >> as >> >> bonded interactions by definition and a table is made internally. >> When >> >> bonded interactions exceed the minimum convention image distance >> (MCID), >> >> then the simulation generally crashes due to a distance which is >> above >> >> the >> >> MCID. >> >> Obviously, Gromacs starts complaining about this issue with a warning >> >> regarding a distance between two atoms which is reasonably large and >> it >> >> assumes that we are performing a free energy calculation. Has anybody >> >> encounter a similar issue before, honestly I would like to find >> another >> >> way to define the interaction between pair of particles as purely >> >> nonbonded potential (with different sigma's parameters) and not as >> >> pairs, >> >> any help will be appreciate! >> >> >> >> kind regards, >> >> >> >> >> >> >> >> -- >> >> Dr. Adolfo Poma >> >> Institute of Physics >> >> Polish Academy of Science >> >> Al. Lotnikow 32/48, >> >> 02-668 Warsaw, Poland >> >> >> >> -- >> >> Gromacs Users mailing list >> >> >> >> * Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> >> posting! >> >> >> >> * Can't post? 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