Dear Justin & Mark, Hi ! I am doing equilibration and again the error comes with the following warnings in the pr.log file,
Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 224.227219 (between atoms 1932 and 1934) rms 4.182889 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 198 200 49.7 0.1449 0.1615 0.1449 200 201 90.1 0.1090 1.2644 0.1090 200 202 46.8 0.1529 0.1690 0.1529 200 211 41.2 0.1522 0.1686 0.1522 ................................ and so on Then Constraint error in algorithm Lincs at step 0 Energies (kJ/mol) Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14 1.55786e+03 1.43449e+01 2.56063e+03 5.34585e+03 1.25360e+04 LJ (SR) LJ (LR) Coulomb (SR) Coul. recip. Position Rest. 2.62155e+05 -1.69778e+03 -6.01840e+05 -1.97421e+21 1.12486e+00 Potential Kinetic En. Total Energy Temperature Pressure (bar) -1.97421e+21 4.12749e+07 -1.97421e+21 1.30857e+05 -4.47584e+17 Step 1 Warning: pressure scaling more than 1%, mu: -2.6855e+10 -2.6855e+10 -2.6855e+10 Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 10042.537109 (between atoms 1932 and 1933) rms 189.576416 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 170 172 63.5 0.1335 0.1514 0.1335 172 173 41.5 0.1449 0.1421 0.1449 172 181 87.7 0.1449 0.2690 0.1449 173 174 38.6 0.1090 0.1403 0.1090 Then Constraint error in algorithm Lincs at step 1 Correcting invalid box: old box (3x3): old box[ 0]={-1.94981e+11, 0.00000e+00, -0.00000e+00} old box[ 1]={ 0.00000e+00, -1.94981e+11, -0.00000e+00} old box[ 2]={ 0.00000e+00, 0.00000e+00, -1.94981e+11} new box (3x3): new box[ 0]={-1.94981e+11, 0.00000e+00, -0.00000e+00} new box[ 1]={ 0.00000e+00, -1.94981e+11, -0.00000e+00} new box[ 2]={ 0.00000e+00, 1.94981e+11, -1.94981e+11} finaly Fatal error: Box was shifted at least 10 times. Please see log-file Now will I start again from the begining by taking PDB file from RCSB ? or something else. I am checking the lincs warning page of gromacs but if you suggest me some correction it will be helpful. Regards, Lal badshah Send instant messages to your online friends http://uk.messenger.yahoo.com
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