[gmx-users] Fwd: »Computational Electrophysiology«

[Harutyun Sahakyan]

Dear Gromacs users,

I am trying to simulate membrane potential using computational
electrophysiology protocol.

I modeled protein-membrane system with charmm-gui, equilibrate it and run
MD simulation. After some steps, I get this error.


=======================================================================
starting mdrun 'Title'
50000000 steps, 100000.0 ps.
SWAP: Performed 35 swaps in step 100 for iontype POT.
SWAP: Performed 14 swaps in step 100 for iontype SOD.
step  200: timed with pme grid 72 72 108, coulomb cutoff 1.200: 2495.3
M-cycles

SWAP: Warning: 12 atoms were detected as being in both channels! Probably
your split
SWAP:          cylinder is way too large, or one compartment has collapsed
(step 200)
SWAP: Performed 1 swap in step 200 for iontype SOD.

SWAP: Warning: 8 atoms were detected as being in both channels! Probably
your split
SWAP:          cylinder is way too large, or one compartment has collapsed
(step 300)
SWAP: Performed 1 swap in step 300 for iontype POT.
SWAP: Performed 1 swap in step 300 for iontype SOD.
step  400: timed with pme grid 64 64 100, coulomb cutoff 1.327: 2610.4
M-cycles

SWAP: Warning: 8 atoms were detected as being in both channels! Probably
your split
SWAP:          cylinder is way too large, or one compartment has collapsed
(step 400)
SWAP: Performed 2 swaps in step 400 for iontype POT.
SWAP: Performed 2 swaps in step 400 for iontype SOD.

SWAP: Warning: 9 atoms were detected as being in both channels! Probably
your split
SWAP:          cylinder is way too large, or one compartment has collapsed
(step 500)
SWAP: Performed 1 swap in step 500 for iontype POT.
SWAP: Performed 2 swaps in step 500 for iontype SOD.
step  600: timed with pme grid 56 56 84, coulomb cutoff 1.538: 3583.0
M-cycles

SWAP: Warning: 8 atoms were detected as being in both channels! Probably
your split
SWAP:          cylinder is way too large, or one compartment has collapsed
(step 600)
SWAP: Performed 2 swaps in step 600 for iontype POT.
SWAP: Performed 1 swap in step 600 for iontype SOD.

SWAP: Warning: 6 atoms were detected as being in both channels! Probably
your split
SWAP:          cylinder is way too large, or one compartment has collapsed
(step 700)
SWAP: Performed 3 swaps in step 700 for iontype POT.

-------------------------------------------------------
Program:     gmx mdrun, version 2018.1
Source file: src/gromacs/swap/swapcoords.cpp (line 1911)

Fatal error:
Could not get index of SOL atom. Compartment contains 3 SOL molecules before
swaps.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
==================================================================



The number of steps before the error depends on ion concentrations in
compartments A and B. Moreover, the number of SOL molecules in the error
message can be different as well.

I have tried to change cylinder parameters however it does not solve the
problem.

Do you have any ideas? Have you faced this error before?

Channels are defined as several amino acids in the central parts of the
channel.

I attached my md.mdp file for more detailed information.



Thanks in advance.

Sincerely,

Harutyun Sahakyan

Senior assistant at Laboratory of

Computational Modeling of Biological Processes,

Institute of Molecular Biology, NAS, Armenia, Yerevan