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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists