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

[Atsutoshi Okabe]

Thanks, Justin.
I tried turning [bonds],  [angles], [dihedrals] interaction on one-by-one. 
However, same errors occurred in all cases.
Also, I tried the calculation on 1 cpu using the following command and the error did not occur!
(that means I did not use parallelization)
gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu

So, I am wondering if the calculation using both [intermolecular-interactions] tool and parallelization can not work and that causes the error messages below.
[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 used the following command for parallelization
mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus


Bests,
Atsutoshi

2015/09/03 5:42、Justin Lemkul <jalemkul at vt.edu> のメール：

> 
> 
> On 9/2/15 10:21 AM, Atsutoshi Okabe wrote:
>> I mean that the entire [intermolecular_interaction] directive were commented out below;
>> ;[ intermolecular-interactions ]
>> 
I tried turning [bonds] or [angles] or [dihedrals] interaction on one-by-one. 
However, same errors occurred in all cases.
Then, I tried the calculation on 1cpu using the following command and the error did not occur!
(that means I do not use parallelization)
gmx_mpi mdrun -deffnm equil$LAMBDA  # 1 cpu

So, I am wondering if the calculation using both [intermolecular-interactions] tool and parallelization can not work and that causes the error messages.
[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 use the following command to use parallelization
mpirun -np 8 gmx_mpi mdrun -deffnm equil$LAMBDA # 8cpus
> 
>> ;[ 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
>> 
>> I checked global atom number in .gro file of protein-ligand complex. It looks no problem.
>> (407, 409 and 411 are atom number of protein,  3172, 3144 and 3152 are atom number of ligand in gro file of complex)
>> Curiously, this error occurs when the vdW interaction between ligand and the environment becomes to turn-off(it means Lambda=0.7~1.0).
>> Conversely, the calculations were finished normally when the vdW interaction remains(it means Lambda=0.0~0.7).
>> 
> 
> I've never tried using [bonds] in this context; the pull code is a better approach.
> 
> Perhaps there's an issue with the negative dihedral?  Have you tried turning these interactions on one-by-one to see if there is a specific entry that leads to a failure?  That's the most surefire way to find it.
> 
> -Justin
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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