[gmx-users] simulation problem whit lincs

[Gerrit Groenhof]

Hi 

Sorry I have no solution to your problem yet, but out of 
curiosity, are you running on an AMD cpu?

Gerrit

> 
> I am doing a simulation of system with one protein and a peptide
> i do all steps necesary for the simulation(minimization, genion
> ,position restrain etc...) when i run the final step(MD) runs whitout
> problem during some time.. these is the error
> Step 161731, time 323.462 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 598.181541 (between atoms 245 and 253) rms 30.851655
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     228    230   71.1    0.1526   0.1637      0.1330
>     230    231   89.9    0.1254   0.1791      0.1000
>     230    232   93.9    0.1431   3.1038      0.1470
>     232    233   55.3    0.1637   3.4467      0.1530
>     232    241  166.2    0.5243  18.0264      0.1530
>     233    234  142.6    0.1816   0.5641      0.1530
>     234    235   63.4    0.1569   0.2542      0.1530
>     235    236   38.4    0.1531   0.2049      0.1530
>     241    242  167.2    0.7252  17.4063      0.1230
>     241    243  174.9    2.5790  33.7894      0.1330
>     243    244  174.5    2.9965  32.4020      0.1000
>     243    245  178.2    5.9836  63.5208      0.1470
>     245    246  169.7    6.5919  56.3915      0.1530
>     245    253  179.0    7.9640  91.6748      0.1530
>     246    247  168.4    2.6903   9.8748      0.1530
>     247    248  164.5    5.1313  20.9254      0.1530
>     248    249  172.3    6.8486  21.0018      0.1230
>     248    250  169.4    6.8948  21.9502      0.1330
>     250    251  116.6    1.2659  10.9623      0.1000
>     250    252  121.4    1.0057  11.1177      0.1000
>     253    254  174.8    4.7518  59.2405      0.1230
>     253    255  177.1    5.0970  68.2804      0.1330
>     255    256  169.2    1.4168  31.4833      0.1000
>     255    257  170.7    1.6224  32.8697      0.1470
>     257    258  161.4    0.3731  16.8051      0.1530
>     257    266  178.5    0.4607  21.1382      0.1530
>     258    259  141.7    0.2932   3.7214      0.1530
>     259    260   52.3    0.2080   0.7846      0.1530
>     260    261   62.1    0.1605   0.1708      0.1530
>     261    262   71.1    0.1480   0.1571      0.1470
>     262    263   47.3    0.1000   0.1444      0.1000
>     262    264   46.5    0.1000   0.1433      0.1000
>     262    265   43.5    0.0999   0.1388      0.1000
>     266    267  168.8    0.2212   9.2796      0.1230
>     266    268  168.9    0.2406   9.6550      0.1330
>     268    269   62.6    0.1641   2.0107      0.1000
>     268    270   41.4    0.2100   2.1612      0.1470
>     270    271  125.0    0.1688   0.1061      0.1530
>     271    272   41.6    0.1264   0.0824      0.1230
>     271    273   64.9    0.1359   0.1026      0.1330
>     273    274   34.5    0.1004   0.1255      0.1000
> Constraint error in algorithm Lincs at step 161731
> 
> Step 161731  Warning: pressure scaling more than 1%, mu: 1.02208 1.02208
> 1.02208
> Grid: -2147483648 x -2147483648 x -2147483648 cells
> 
> 
> 
> 
> 
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