disrepancy between dccm values

[swastik phulera]

Hi, If i compare the plots obtained from cm obtained by doing

cm <- dccm(modes)

vs

if i read the mode7 (obtained from Normal modes analysis as a pdb and converted to dcd using an external program mdconvert) as a dcd trajectory and then calculate

dcd<-read.dcd("mode7.dcd") cm<- dccm(dcd)

Now in principal these two plots should be exactly the same, but what I see is that although the general trends are similar the values are off by a factor of 2.

[Lars Skjærven]

Hi Swastik, The function call to dccm(modes) will use all normal modes to calculate the correlations. Using dccm(xyz) will use only that trajectory, so only mode 7. The latter will also not be weighted by its eigenvalue. Lars