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

[poma at ifpan.edu.pl]

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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