[gmx-users] Larger simulation times because of many [ pairs ]?

Mark Abraham mark.j.abraham at gmail.com
Sat Feb 14 11:08:09 CET 2015


Without having checked the code, adding [pairs] forces mdrun to compute
that non-bonded interaction. So you should expect the cost of computing
those interactions to go up. If that dominates the cost of the simulation
(e.g. you have no other non-bonded interactions) then your observations are
consistent. The implementation of [pairs] is not optimized for this


On Fri, Feb 13, 2015 at 11:13 PM, Fernando Yrazu <fyrazu at rice.edu> wrote:

> Hi,
> I am bulding a C-alpha coarse grained model of a protein, and I would like
> to use a modified Lennard-Jones potential for every possible non-bonded
> contact.  For that purpose, I have built a list of all the possible pairs
> under the [ pairs ] heading of the topol.top file.
> Before, I used this strategy for a model with about 300 non bonded
> parameters and it worked fine. Now that I am using about 6400 non bonded
> parameters (all of them listed under the [ pairs ] heading), simulations
> take about 10 times longer to complete. There is still only one table for
> all of the contacts.
> Given that I am only changing the factor by which I multiply the geometric
> part of the potential for each pair (meaning, a single table is read), I
> wonder whether this large increase in computation time is expected. The
> Gromacs 4.6.7 manual (section 3.4 - page 15), when referring to energy
> monitor groups, states that:
> "All non-bonded interactions between pairs of energy-monitor groups can be
> excluded (see sec. 7.3). Pairs of particles from excluded pairs of
> energy-monitor groups are not put into the pair list. This can result in a
> significant speedup for simulations where interactions within or between
> parts of the system are not required.”
> Therefore, my question is whether adding a large number of pairs to the
> list (even when using a single potential table) can result in such a
> slowdown of the simulations.
> Thank you,
> Fernando Yrazu
> PhD student
> Rice University
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