[gmx-users] Free energy calculation using inter-molecular bonded interaction

[Atsutoshi Okabe]

Hi all,

I have a question about how to use inter-molecular bonded interaction tool in GROMACS 5.1.
I want to calculate binding free energy between protein and ligand adding harmonic restraint force to prevent the ligand from leaving the binding site when the native ligand-receptor interaction are turned off.

So, I added [ intermolecular-interactions ] in complex topology file below.
[ molecules ]
; Compound        nmols
protein            1
CRW                3
ligand             1
SOL         11266
CL               5

[ intermolecular-interactions ]

[ bonds ]
411 3173  6  0.55  2090

[ angles ]
411 3173 3152  1  164.5  20.9
409 411 3173  1  122.3  20.9

[ dihedrals ]
409 411 3173 3152  2  12.0  20.9
407 409 411 3173  2  75.6  20.9
411 3173 3152 3144  2  -126.0  20.9

However, I got the following error.

Reading file equil1.00.tpr, VERSION 5.1 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1

Using 8 MPI processes
Using 1 OpenMP thread per MPI process

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity
[proxy:0:0 at leon304] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:70): assert (!(pollfds[i].revents & ~POLLIN & ~POLLOUT & ~POLLHUP)) failed
[proxy:0:0 at leon304] main (./pm/pmiserv/pmip.c:387): demux engine error waiting for event
[mpiexec at leon304] HYDT_bscu_wait_for_completion (./tools/bootstrap/utils/bscu_wait.c:101): one of the processes terminated badly; aborting
[mpiexec at leon304] HYDT_bsci_wait_for_completion (./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned error waiting for completion
[mpiexec at leon304] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error waiting for completion
[mpiexec at leon304] main (./ui/mpich/mpiexec.c:548): process manager error waiting for completion

I tried to comment out the lower row involving [ intermolecular-interactions ] in the topology file and confirmed that the calculation was finished normally.
(Of course, the ligand was leaving from the binding site when the ligand-receptor interaction are completely turned off.)
Could you advice me how to solve this error?

Thank you,
Atsutoshi Okabe