<html><div style='background-color:'><DIV class=RTE>Dear all,<BR>I'm trying to study the conformational freedom of a proteic system using the CONCOORD algorithm. Hence I've energy minimized the protein in a water box using the OPLS force field and then I've put the minimized structure in a new gro file without the water molecules.<BR>Then I've runned the cdist command on this new gro file including the hyderogen bond index file (-n option) and using -measure 20. The other parms are ste as default.<BR>But the structures generated by disco command (with default options) are very similar (backbone rmsd=0.237 A).<BR>Hence I've tried to repeat the cdist command using -measure 20 and -nm 0.5 (default 0.05) but the 100 structures generated by disco are unconverged.<BR>How can I set new parms to improve the conformational space sampling?<BR>Thanks in advance,<BR>Vincenzo</DIV></div><br
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