[gmx-users] position restrain dynamics error

[Subramaniam Boopathi]

Dear Sir,
        I am succesfully run molecules upto energy minimization, in case of
position restrain md step , i have following, could you help to overcome
the A charge group moved too far between two domain decomposition steps.

Step 1, time 0.002 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.021061, max 0.387149 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   90.0    0.0960   0.1332      0.0960

Step 2, time 0.004 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.034712, max 0.636602 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   90.1    0.1332   0.1571      0.0960

Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1#

Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1#
Wrote pdb files with previous and current coordinates

Step 3, time 0.006 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.023755, max 0.423951 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   90.0    0.1571   0.1367      0.0960

Step 4, time 0.008 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.051081, max 0.931870 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   90.3    0.1367   0.1855      0.0960

Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1#

Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1#
Wrote pdb files with previous and current coordinates

Step 5, time 0.01 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.020335, max 0.372790 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   89.9    0.1855   0.1318      0.0960

Step 6, time 0.012 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.056021, max 1.029913 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   90.2    0.1318   0.1949      0.0960

Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2#

Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2#
Wrote pdb files with previous and current coordinates

Step 7, time 0.014 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.024586, max 0.451876 (between atoms 360 and 363)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
    360    363   90.0    0.1949   0.1394      0.0960

with regards
S. Boopathi