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