[gmx-users] Simulation crashes: issue with [pair] potential

Fri Mar 3 09:52:52 CET 2017

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 <poma at 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 <poma at 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
>> >>
>> >> --
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