[gmx-users] 9 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

[ajani haresh]

Respected Sir,





Myself Haresh  Ajani from National Institute of Pharmaceutical Education &
Research.



I am using gromacs version 4.5.3. I am working on molded Protein.



I am facing one problem in gromacs after minimization of the protein.



I have put my query here.





Fatal Error : Wrote pdb files with previous and current coordinates



Warning: 1-4 interaction between 687 and 691 at distance 4.001 which is
larger than the 1-4 table size 2.000 nm



These are ignored for the rest of the simulation



This usually means your system is exploding,



if not, you should increase table-extension in your mdp file



or with user tables increase the table size



Fatal error:



9 particles communicated to PME node 5 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.



This usually means that your system is not well equilibrated.





I have given run for gromacs.



Pdb2gmx -f 1.pdb -o 12.pdb -p 12.top -ignh -ter -missing

then I have selected gromos force field and SPC water model.



editconf -bt cubic -f 12.pdb -o 123.pdb -c -d 0.9



genbox -cp 123.pdb -cs spc216.gro -p 123.top -o 123_b4ion.pdb



 then neutralize the protein and  energy minimization.









Steepest Descents:



   Tolerance (Fmax)   =  1.00000e+03



   Number of steps    =         3500







writing lowest energy coordinates.







Steepest Descents converged to Fmax < 1000 in 3468 steps



Potential Energy  = -9.6223600e+05



Maximum force     =  9.3264703e+02 on atom 695



Norm of force     =  2.5498827e+01







Step 0, time 0 (ps)  LINCS WARNING



relative constraint deviation after LINCS:



rms 0.003107, max 0.020384 (between atoms 642 and 643)



bonds that rotated more than 30 degrees:



 atom 1 atom 2  angle  previous, current, constraint length



starting mdrun 'MD_loweng_model1 in water'



12500 steps,     25.0 ps.







Step 0, time 0 (ps)  LINCS WARNING



relative constraint deviation after LINCS:



rms 18.316392, max 238.458267 (between atoms 695 and 696)



bonds that rotated more than 30 degrees:

 atom 1 atom 2  angle  previous, current, constraint length

    685    686   30.9    0.1530   0.1317      0.1530

    686    687   60.3    0.1531   0.2200      0.1530

    687    688   64.2    0.1534   1.3927      0.1530

    629    631   62.2    0.1332   0.2212      0.1330

    629    630   32.4    0.1231   0.1531      0.1230

    631    633   80.2    0.1476   1.2395      0.1470

    631    632   73.3    0.1001   0.1563      0.1000

    633    650   64.8    0.1536   1.1461      0.1530

    633    634   84.1    0.1561   2.3556      0.1530

    634    635   38.9    0.1557   6.0052      0.1530

    635    638   85.4    0.1413   6.8134      0.1390

    635    636   90.6    0.1344  12.6580      0.1330

    636    639   37.3    0.1336   7.0188      0.1330

    636    637  149.3    0.1099   8.2681      0.1090

    638    642   54.8    0.1404   1.8808      0.1390

    638    641   70.5    0.1405   1.9874      0.1390

    639    641  119.2    0.1342   5.2357      0.1330

    639    640  118.9    0.1009   3.3865      0.1000

    641    644   68.6    0.1402   1.9737      0.1390

    642    646   68.7    0.1417   0.2159      0.1390

    642    643   54.0    0.1112   0.1584      0.1090

    644    648   81.7    0.1406   1.3960      0.1390

    644    645   72.1    0.1103   0.8079      0.1090

    646    648   65.5    0.1398   0.5901      0.1390

    648    649   67.1    0.1096   0.4282      0.1090

    688    689  132.4    0.1490   1.4233      0.1470

    689    690  151.7    0.1012   0.7597      0.1000

    691    695   78.6    0.1357  22.8056      0.1340

    691    692   57.4    0.1327   3.6809      0.1340

    692    694  151.9    0.1014   0.5744      0.1000

    692    693  165.2    0.1014   0.7382      0.1000

    695    697  119.6    0.1012  18.8779      0.1000

    695    696   86.1    0.1012  23.9458      0.1000

    652    654   42.0    0.1471   0.2030      0.1470

    652    653   50.7    0.1001   0.1549      0.1000

    650    652   72.6    0.1333   0.2537      0.1330

    650    651   69.2    0.1232   0.1942      0.1230

Wrote pdb files with previous and current coordinates



Warning: 1-4 interaction between 687 and 691 at distance 4.001 which is
larger than the 1-4 table size 2.000 nm



These are ignored for the rest of the simulation



This usually means your system is exploding,



if not, you should increase table-extension in your mdp file



or with user tables increase the table size







Fatal error:



9 particles communicated to PME node 5 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.



This usually means that your system is not well equilibrated.




-- 
Haresh Ajani
09925522578
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