Dear users,<br> <br> I ran 100ns simulation for 4 proteins, 3 of them were <br>non covalent dimers in solution, but only 1 is a covalent <br>dimer connected by a disulphide bridge. I used monomers<br>to run the job. <br>
Only in the case of covalent dimer I was getting severe <br>minimum image violation ie. out of 50001 data points, <br>282 are <= 1.4nm<br>280 are < 1.4nm<br>144 are < 1.3nm<br>79 are < 1.2nm<br>28 are < 1.1nm<br>
4 < 1.0nm<br><br>I agree that this is quite wrong but I wanted to know whether<br>any useful information can be gathered out of this simulation?<br> <br>In another data while calculating the energy terms it gives<br>nan (not a number error) for rmsd alone eg - <br>
Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Temperature 300 9e-05 -nan -0.000501989 (K)<br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Pressure 0.99914 0.027 -nan 0.0174391 (bar)<br>
<br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>Volume 517.755 0.0094 -nan 0.010871 (nm^3)<br>
<br>Initially i though some data points are missing but later <br>gmxcheck gives that all the data points are present.<br>now what could be the error? <br><br>I had asked this question before and was instructed to check the <br>
trajectory. I checked the rmsd rmsf of this with the other proteins<br>it similar but one of the segment has high rmsf compared to the other<br>proteins.<br><br>Thanking you<br>With regards<br>M. Kavyashree<br><br><br><br>