Hi, The problem is that all vdw and electrostatic pairs are precomputed in the current implementation. Setting cut-off values doesn't change this. To make the OB force fields work with large amounts of atoms, the non-bonded pairs should be detected dynamically.
Tim On Wed, May 16, 2012 at 6:17 PM, Tom Daff <td...@uottawa.ca> wrote: >> Isn't there some way to turn down the VdW via a distance cutoff or so? > (EnableCutOff and SetVdWCutoff) I've never used these but hopefully they > will prevent the pairwise generation of all of the VdW terms. > > Curiously, this doesn't work. Enabling the cutoffs and setting to very small > values still runs into the same memory problems. I may be wrong, but it > seems that in forcefielduff.cpp:1417, if the atoms are not in _interGroups > then the BitIsOn set by the cutoff will not be checked and > SetupVDWCalculation is still called for every pair. I assume that the groups > are not automatically generated? Fortunately, in my case, I have worked out > that creating an OBConstraints and AddIgnore for every atom does exclude > them from the vdW, but maybe this is a bug? > > Tom > > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
