probably a bad starting structure... check this website for pressure scaling warning : http://wiki.gromacs.org/index.php/Errors
regards, pawan On Mon, Apr 27, 2009 at 5:21 PM, Sheetal Arora <[email protected]>wrote: > 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 > > _______________________________________________ > gmx-users mailing list [email protected] > 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 >
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