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

[Justin Lemkul]

On 9/1/15 10:12 AM, Atsutoshi Okabe wrote:
> Thanks, Justin.
> I want to add restraint between protein and receptor using [intermolecular-interactions] section(not comment out [bonds], [angles] [dihedrals] lines)in new support tool of GROMACS 5.1.
> But I got the error below and I don’t know what causes the problem.
>

I understand what you want to do; I tested this code before it was merged so I 
certainly know how it works :)

I'm seeking clarification on what you said before:

You said: "I tried to comment out the lower row involving [ 
intermolecular-interactions ] in the topology file and confirmed that the 
calculation was finished normally."

What does this mean?  The last line *only* or the entire 
[intermolecular_interactions] directive?  "Lower row" is not clear.

The simplest check is to make sure your global atom numbers are right; if they 
aren't then the physics will of course be unsound.

-Justin

> Bests,
> Atsutoshi
>
> 2015/09/01 11:17、Justin Lemkul <jalemkul at vt.edu> のメール：
>
>>
>>
>> On 8/31/15 11:20 AM, Atsutoshi Okabe wrote:
>>> 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?
>>>
>>
>> You mean when you comment out all of the intermolecular interactions, or literally just the last line.  If the latter, then you've found your problem.
>>
>> -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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-- 
==================================================

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

==================================================