[gmx-users] position restrain problem

[Yang Ye]

It is seen that the atoms belongs to water. Did you get any error from 
grompp? Did you used the same water .itp in your topology as the one you 
used with genbox? There are other possibilities.

Yang Ye

Anthony Cruz wrote:

>Hi:
>I am trying to run a position restrain dynamics of a protein that have 3 
>parts. The energy minimization run for only 44 steps. When I try to run the 
>position restrain I have the following error:
>
>Step 6, time 0.012 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>max 0.011542 (between atoms 1462 and 1463) rms 0.000543
>bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>     62     63   32.3    0.0992   0.1000      0.1000
>    305    306   35.2    0.0992   0.0998      0.1000
>    354    355   30.3    0.1320   0.1330      0.1330
>    381    382   31.2    0.0992   0.1000      0.1000
>    580    581   40.9    0.0992   0.1000      0.1000
>   1407   1409   30.2    0.0995   0.1003      0.1000
>   1410   1412   54.3    0.0997   0.0992      0.1000
>   1462   1463   79.8    0.0994   0.1012      0.1000
>   1462   1464   43.7    0.0997   0.1007      0.1000
>   1493   1495   32.2    0.0994   0.0997      0.1000
>   1542   1543   31.4    0.0990   0.0996      0.1000
>   1698   1699   34.5    0.0992   0.1000      0.1000
>   1861   1863   35.3    0.0992   0.0997      0.1000
>   1866   1867   30.1    0.0993   0.1000      0.1000
>   2010   2012   30.0    0.0993   0.0997      0.1000
>
>t = 0.012 ps: Water molecule starting at atom 3861 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
>previous and current coordinates
>Large VCM(group rest):     -0.00645,     -0.00647,      0.00685, ekin-cm:  
>3.95311e+01
>
>Step 7, time 0.014 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>max 0.013635 (between atoms 1462 and 1464) rms nan
>bonds that rotated more than 30 degrees:
> atom 1 atom 2  angle  previous, current, constraint length
>    305    306   34.5    0.0991   0.0999      0.1000
>    669    670   33.5    0.1081   0.1089      0.1090
>    862    863   48.7    0.0992   0.1002      0.1000
>   1358   1359   37.3    0.0994   0.1004      0.1000
>   1407   1409   31.8    0.0995   0.1001      0.1000
>   1410   1412   34.1    0.0985   0.0995      0.1000
>   1447   1448   34.6    0.1083   0.1093      0.1090
>   1462   1463   71.5    0.1004   0.0993      0.1000
>   1462   1464   30.6    0.0999   0.0986      0.1000
>   1648   1649   44.7    0.1080   0.1086      0.1090
>   1825   1826   30.0    0.1083   0.1092      0.1090
>   1842   1843   36.3    0.0993   0.1001      0.1000
>   1866   1867   30.7    0.0993   0.0999      0.1000
>   2010   2011   44.7    0.0992   0.0999      0.1000
>   2010   2012   37.2    0.0990   0.0992      0.1000
>
>t = 0.014 ps: Water molecule starting at atom 3666 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
>previous and current coordinates
>
>How I can solve the problem???
>
>Best regards
>
>Anthony
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>  
>

-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/