Hi everybody, during the mdrun_mpi I get many LINCS warnings like for example:
Step 1143, time 1.143 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.265373, max 1.416702 (between atoms 976 and 979) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 976 979 90.0 0.1072 0.2320 0.0960 But I don't know why. I already minimized my protein. And also in the grompp run there were no error messages. This was the end of my grompp output: processing index file... Making dummy/rest group for Acceleration containing 80212 elements Making dummy/rest group for Freeze containing 51274 elements Making dummy/rest group for VCM containing 80212 elements Number of degrees of freedom in T-Coupling group System is 102623.00 Making dummy/rest group for User1 containing 80212 elements Making dummy/rest group for User2 containing 80212 elements Making dummy/rest group for XTC containing 80212 elements Making dummy/rest group for Or. Res. Fit containing 80212 elements Making dummy/rest group for QMMM containing 80212 elements T-Coupling has 1 element(s): System Energy Mon. has 2 element(s): Protein non-Protein Acceleration has 1 element(s): rest Freeze has 2 element(s): Protein_&_!TYP rest User1 has 1 element(s): rest User2 has 1 element(s): rest VCM has 1 element(s): rest XTC has 1 element(s): rest Or. Res. Fit has 1 element(s): rest QMMM has 1 element(s): rest Checking consistency between energy and charge groups... Estimate for the relative computational load of the PME mesh part: 0.32 writing run input file... Can you please help me? Thank you, Eva -- 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