disrepancy between dccm values
Issue #351
resolved
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.
Comments (2)
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Hi Swastik, The function call to
dccm(modes)
will use all normal modes to calculate the correlations. Usingdccm(xyz)
will use only that trajectory, so only mode 7. The latter will also not be weighted by its eigenvalue. Lars