黄永棋 wrote: > Hi > > I was trying to do a protein simulation with the protein embedded in a > dopc bilayer , but the mdrun killed with a message like this: > > " Step 124772, time 249.544 (ps) LINCS WARNING > relative constraint deviation after LINCS: > max 78.497551 (between atoms 28341 and 28343) rms 0.598885 > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 28332 28333 170.9 0.1000 0.9127 0.1000 > 28335 28336 30.4 0.1000 0.7634 0.1000 > 28335 28337 179.8 0.1000 6.4688 0.1000 > 28341 28342 140.6 0.1000 0.7312 0.1000 > 28341 28343 179.7 0.1000 7.9498 0.1000 > Constraint error in algorithm Lincs at step 124772 > Wrote pdb files with previous and current coordinates > > Segmentation fault " > > > I checked the gro. file and found these are water molucules . Can > anybody tell me why this happened and what shall I do to aviod this ?
Searching the mailing list for "LINCS WARNING" or similar would have found the other ten thousand posts where people have been advised to minimise their system better before equilibrating, or equilibrate better before simulating, as well as suggestions that you describe your system preparation methodology so that we don't have to read your mind. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
