[gmx-users] Increase the box size or decrease rlist

pragna lakshmi pragnapcu at gmail.com
Tue Aug 19 20:14:12 CEST 2014

Dear all,
I am trying to do MD simulation of POPC membrane simulation with peripheral
attachment of protein ligand complex. Steps that i have performed so far

1. orienting the protein with editcong -princ command
2. rotating it along the y-axis with editconf -rotate 0 40 0 command
3. separation of protein ligand files into individual files and generation
of topology file of protein from pdb2gmx and ligand from swissparam.
(charmm 36ff was used for protein topology generation. source:
http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs )
4. The protein and ligand files were merged followed by necessary changes
in topology file.
5. Pre-equilibrated POPC bilayer was downloaded from Dr.Klauda's website
whereas its itp file was taken from Stockholm_Lipids website.
6. After this, when i am running the command
grompp -f minim.mdp -c POPC.gro -p POPC.top -o em_POPC.tpr
i am facing the fatal error:
ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rlist.
As it is suggesting, I have decreased rlist, rcoulomb and rvdw from 1.2 to
1.0. But still the same error is raising.

I would be so thankful, if someone shows me the source of this problem and
its solution.

Thanking You,

Pragna Lakshmi.T,
Ph.D. Scholar,
IPLS Project,
Pondicherry University,
India - 605014.

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