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? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-requ...@gromacs.org. > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
