hi<br><br> i gave energy minimization for 3000 steps but it runs only 1906 steps. these are the files (em.trr, em.edr, em.log) i got after energy minimization. my energy values are<br>P.E = -2.6755090e+06<br>Maximum force = 9.6265039e+02 an atom 5483<br>
Norm of force = 1.263261.9e+01<br><br> while doing position restrain with these files i got error like<br><br>WARNING 1 [file pr.mdp, line unknown]:<br> Unknown or double left-hand 'warnings' in parameter file<br>
NOTE 1 [file top.top, line 41]:<br> System has non-zero total charge: -3.400000e+01<br><br>by using -maxwarn option i ignored the warnings and gone for mdrun it gives error like this<br><br>starting mdrun 'Protein in water'<br>
500 steps, 1.0 ps.<br>step 400, remaining runtime: 150 s <br>Step 416, time 0.832 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.000996, max 0.006287 (between atoms 5428 and 5430)<br>
bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 12635 12636 30.1 0.1104 0.1093 0.1090<br> 10211 10213 38.3 0.1104 0.1097 0.1090<br><br>
Step 423, time 0.846 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.025639, max 2.318898 (between atoms 8806 and 8807)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
8278 8281 31.7 0.1090 0.1090 0.1090<br> 7545 7546 36.4 0.1087 0.1090 0.1090<br><br>hi justin u told me to check the output configuration. i didn't get this line could u tell me which output i have to check.<br>
i loaded the em.gro file in vmd there is no changes in structure.<br><br>looking forward for a reply. thanks in advance.<br><br>cheers,<br><br>Manju.<br><br><br><br><br><br>