I am trying to run the simulation of protein ligand complex. But after running the mdrun by giving command-"grompp –f md. mdp –c pr.gro –p trp.top –o md.tpr " and then "nohup mdrun –deffnm md & " the md.log file is showing the following message- Step 11 Warning: pressure scaling more than 1%, mu: 1.01684 1.01684 1.01684
Step 13 Warning: pressure scaling more than 1%, mu: 0.947161 0.947161 0.947161 Step 14 Warning: pressure scaling more than 1%, mu: 1.01207 1.01207 1.01207 Step 15 Warning: pressure scaling more than 1%, mu: 1.18248 1.18248 1.18248 Step 16 Warning: pressure scaling more than 1%, mu: 0.867467 0.867467 0.867467 Step 16, time 0.032 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.099556 (between atoms 1396 and 1398) rms 0.028595 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 21 23 30.8 0.1740 0.1569 0.1470 38 40 32.0 0.1740 0.1583 0.1470 54 56 33.0 0.1740 0.1588 0.1470 56 57 30.6 0.1810 0.1623 0.1530 67 69 31.4 0.1740 0.1568 0.1470 104 106 32.6 0.1740 0.1588 0.1470 106 107 31.1 0.1811 0.1632 0.1530 216 218 31.8 0.1741 0.1584 0.1470 I am attaching my md.mdp file.Please help me in this regard. -- Sheetal Arora M.Tech(Biotechnology & Medical Engg) NIT Rourkela
md.mdp
Description: Binary data
_______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php