[gmx-users] Computational electrophysiology, implicit solvent and coarse-grained system: atom/molecule definitions?

Vries, de, H.W. h.w.de.vries.6 at student.rug.nl
Tue Mar 14 11:19:13 CET 2017

Dear all,

I am currently trying to run the computational electrophysiology scheme on
an implicit solvent, coarse-grained system by introducing a little

In the manual, it is stated that we can tell the routine what molecules are
'solvent', and what molecules are 'ions' through custom index groups. As my
system thus does not have water molecules, I inserted non-interacting dummy
particles into the system, which I then tell the CompEl scheme to use as a
solvent group for swapping (via custom index groups)

However, the simulation gets stuck at:

SWAP: Making sure each atom belongs to at most one of the swap groups.
SWAP: Checking whether all ion molecules consist of 20012 atoms
SWAP: Checking whether all solvent molecules consist of 20012 atoms
SWAP: Opening output file swapions.xvg
SWAP: Determining initial ion counts.

Looking at swapions.xvg, I see that the routine doesn't recognize my
coarse-grained atoms correctly: 4800,7206 and 800 are the correct numbers
of coarse-grained atoms that I put in, with 20012 being the total number of
coarse-grained beads that I have in my system:

# ion group contains 4800 atoms with 20012 atoms in each molecule.
# split0 group contains 7206 atoms.
# split1 group contains 7206 atoms.
# solvent group contains 800 atoms with 20012 atoms in each molecule.

Can anyone give me a pointer as to what might be going wrong (I can send
the files directly if requested)? Could this be an issue with the
coarse-grained model im employing, that it is not defined properly in my
topology, or is CompEl really incompatible with any implicit solvent
CG-representation that tries to use dummy particles for swapping purposes?

Thank you kindly,

Henry de Vries

Henry de Vries
Student Topmaster Nanoscience
Micromechanics of Materials Group
tel: +31 (0)6-30520328
office: X5113.0129
Nijenborgh 4, 9747AG
Groningen, Netherlands

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