[gmx-users] Different Cutoff Options

PaulC paul.caheny at uk.fujitsu.com
Wed May 22 17:24:34 CEST 2013


I'm trying to understand how best to compare performance of Gromacs 4.6.1 on
CPU only versus CPU plus GPU on a cluster. Each node has is 2 x 8 Core Sandy
Bridge + 1 Nvidia M2090.

I've been trying to use the d.dppc benchmark (with modifications). I would
like to profile both standard cutoff and pme electrostatics on the CPU and
GPU (as this is building on benchmarking work done on the CPU only which
used these benchmarks). While I have successfully run modifications of the
d.dppc benchmark utilising both the CPU and GPU I have some questions about
the different options.

As a beginner with MD and Gromacs could somebody elaborate on the table
comparing Group and Verlet schemes on this page:


In particular the table shows which non-bonded interaction features are
supported by both the group and verlet schemes.

In the table we see four different 'cutoff' non-bonded interaction features

unbuffered cut-off scheme	 
buffered cut-off scheme
exact cut-off

If plain 'cut-off' is not one of the three more specific schemes listed
above it, how does it differ from each of them?

The d.dppc input file as provided is:

title                    = dppc
cpp                      = /lib/cpp
integrator               = md
nsteps                   = 5000
nstlist                  = 10
nstxout                  = 0
nstvout                  = 0
nstxtcout                = 0
nstlog                   = 0
dt                       = 0.002
constraints = all-bonds
nstenergy                = 0
ns_type                  = grid
coulombtype              = cut-off
rlist                    = 1.0
rvdw                     = 1.0
rcoulomb                 = 1.8
tcoupl                   = berendsen
tc_grps                  = dppc sol
tau_t                    = 0.1 0.1
ref_t                    = 323 323
Pcoupl                   = no

Could you say which of the four cutoff types mentioned above these settings
equate to and how these setting should be changed to equate to each of the
other three cutoff types?

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