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

Kutzner, Carsten ckutzne at gwdg.de
Wed Mar 15 17:12:23 CET 2017


> On 14 Mar 2017, at 11:18, Vries, de, H.W. <h.w.de.vries.6 at student.rug.nl> wrote:
> Dear all,
> I am currently trying to run the computational electrophysiology scheme on
> an implicit solvent, coarse-grained system by introducing a little
> workaround:
> 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.
How does your topol.top file look like? It should list the correct
number of copies of each ion / molecule.

Is this the most recent version (2016)?


> 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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