<html><div style='background-color:'><DIV class=RTE>Dear all,</DIV>
<DIV class=RTE>I've performed a combined ED analysis on a protein free and bound to 4 different ligands.</DIV>
<DIV class=RTE>Hence I've performed 5 MD simulation of 4 ns. Since I've found that all the simulations show a rmsd plateau between 2.4 and 4 ns, I've used this time interval for the concatenation.</DIV>
<DIV class=RTE>Then I've computed the rms fluctuations of the 5 separate trajectories along the first 10 concatneted eigenvectors found with g_covar command.</DIV>
<DIV class=RTE>The major differences are in the 5th eigenvector, where:</DIV>
<DIV class=RTE> </DIV>
<DIV class=RTE> trj 1 trj2 trj3 trj4 trj5</DIV>
<DIV class=RTE>rmsf (nm) 0.052 0.011 0.018 0.013 0.018</DIV>
<DIV class=RTE> </DIV>
<DIV class=RTE>Are the differnces meaningful values?</DIV>
<DIV class=RTE>Do you think these rmsf values are too small?</DIV>
<DIV class=RTE> </DIV>
<DIV class=RTE>Thanks in advance,</DIV>
<DIV class=RTE>Vincenzo</DIV>
<DIV class=RTE> </DIV>
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