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

Fernando Yrazu fyrazu at rice.edu
Fri Feb 13 23:13:48 CET 2015


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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