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

[REMYA R]

Yes sir, even though its not working


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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