[gmx-users] Getting Fatal Error while running simulation of Protein-Ligand complex, at the stage of generating nvt.gro

[Justin Lemkul]

On 4/17/16 12:42 PM, REMYA R wrote:
> Yes sir, even though its not working
>

You're going to have to provide a more complete explanation of what you're 
doing.  What steps you took, .mdp files, how you generated the ligand topology, 
etc.  Simply saying that the system crashed is inadequate to get any useful 
help.  Please also tell us what diagnostic information you can obtain by 
following the suggestions you have probably found online.

-Justin

>
> On Sun, Apr 17, 2016 at 9:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/17/16 11:35 AM, REMYA R wrote:
>>
>>> Dear sir,
>>>
>>> I am getting error  while running simulation of Protein-Ligand complex ,
>>> usong GROMOS force field, spc water model  at the equilibration phase of
>>> bevan lab tutorial for protein-ligand simulation, version 4.6.1 (
>>>
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/06_equil.html
>>> )
>>>
>>> Here below I am pasting some information from em.log
>>>    D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S
>>>
>>>    av. #atoms communicated per step for force:  2 x 48020.5
>>>
>>>
>>>        R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G
>>>
>>>    Computing:         Nodes     Number     G-Cycles    Seconds     %
>>> -----------------------------------------------------------------------
>>>    Domain decomp.        15        152       11.010        2.4     4.9
>>>    DD comm. load         15          1        0.004        0.0     0.0
>>>    Send X to PME         15        125        0.069        0.0     0.0
>>>    Comm. coord.          15        125        5.553        1.2     2.5
>>>    Neighbor search       15        125       21.088        4.6     9.4
>>>    Force                 15        125       21.412        4.6     9.6
>>>    Wait + Comm. F        15        125       20.474        4.4     9.2
>>>    PME mesh               9        125       19.929        4.3     8.9
>>>    Wait + Comm. X/F       9                  31.486        6.8    14.1
>>>    Wait + Recv. PME F    15        125        1.507        0.3     0.7
>>>    Constraints           15        249        1.062        0.2     0.5
>>>    Comm. energies        15        125        2.644        0.6     1.2
>>>    Rest                  15                  87.106       18.9    39.0
>>> -----------------------------------------------------------------------
>>>    Total                 24                 223.343       48.4   100.0
>>> -----------------------------------------------------------------------
>>> -----------------------------------------------------------------------
>>>    PME redist. X/F        9        250        4.982        1.1     2.2
>>>    PME spread/gather      9        250        6.790        1.5     3.0
>>>    PME 3D-FFT             9        250        5.999        1.3     2.7
>>>    PME solve              9        125        2.152        0.5     1.0
>>> -----------------------------------------------------------------------
>>>
>>> Parallel run - timing based on wallclock.
>>>
>>>                  NODE (s)   Real (s)      (%)
>>>          Time:      2.016      2.016    100.0
>>>                  (Mnbf/s)   (GFlops)   (steps/hour)
>>> Performance:    337.723     47.730       223242.7
>>> Finished mdrun on node 0 Thu Apr 14 19:38:14 2016
>>>
>>> I am new user for this simulation, could you please help me to rectify
>>> this
>>> error.Below I am pasting the error message that I got,
>>> *Fatal error:*
>>> A charge group moved too far between two domain decomposition steps
>>> This usually means that your system is not well equilibrated
>>>
>>>
>> Have you tried Google?  This error comes up almost daily on this list...
>>
>> -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

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