[gmx-users] Infinite cutoffs with periodic boundary condition

이종화(Jong Wha Lee) jongwha12 at postech.ac.kr
Mon Jan 12 11:53:48 CET 2015

Dear Gromacs users,


Hello everyone. I am currently trying to simulate a molecule in carbon
dioxide gas. To maintain carbon dioxide near my molecule of interest at a
well-defined pressure, it was necessary to apply periodic boundary
condition. Then, I tried to apply infinite cutoffs (calculate all
interactions) as this would be more accurate with small increase in the
computational costs, considering that I am simulating the gas phase with
small number of atoms.


However, I found that it was not possible to give infinite cutoffs with
periodic boundary condition. Consequently, I decided to use a very large
cutoff (20 nm) and update neighbor list every step to minimize possible
errors from simulation. But this resulted in high computational cost. Could
you suggest any more efficient and accurate methods that I could try?


I attached my .mdp file below. I’m performing NVE simulation after
equilibration with NPT.


integrator           = md

nsteps                 = 50000000       

dt                       = 0.001

; Output control

nstxout               = 50000

nstvout               = 50000

nstenergy           = 5000

nstlog                 = 50000

nstxtcout            = 5000


; Noncovalent interactions and neighbor search

cutoff-scheme    = group

coulombtype      = cut-off

vdwtype            = cut-off


ns_type              = simple

nstlist                 = 1

rlist                     = 20

rcoulomb            = 20

rvdw                  = 20


; No temperature and pressure coupling

tcoupl                 = no

tc-grps                = System

tau_t                  = 0.1

ref_t                   = 298 

pcoupl                = no


pbc                     = xyz

gen_vel              = no

continuation      = yes


Many thanks in advance,


Jong Wha

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