Vyacheslav
kreme_vg@chemy.kolasc.net.ru
On Thu Apr 8 '10 3:10pm, Alex Granovsky wrote
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>Hi,
>if you look into Firefly's output, you'll see:
>
----------------------------------------------- STATISTICS ON AUTOMATIC COORDINATE GENERATION ----------------------------------------------- NUMBER OF USER SPECIFIED BONDS 0 NUMBER OF AUTOGENERATED H-BONDS 0 NUMBER OF BONDS 319 NUMBER OF ANGLES KEPT 1474 NUMBER OF ANGLES DELETED 1 NUMBER OF TORSIONS KEPT 9880 NUMBER OF TORSIONS DELETED 98 NUMBER OF OUT OF PLANE BENDS KEPT 1652 NUMBER OF OUT OF PLANE BENDS DELETED 23 NUMBER OF GENERATED PSEUDOBONDS 154 NUMBER OF EXTRA COORD. 0 NUMBER OF EXTRA COORD. FOR CONSTRAINTS 0 NUMBER OF CONSTRAINED COORD. 0 TOTAL NUMBER OF PRIMITIVES 13325 -----------------------------------------------
>The number of primitives is really huge (esp. torsions).
>The construction of DLCs requires some steps that use
>several square arrays with dimension equal to the number
>of primitives... so the memory requirements are huge as
>well.
>Basically, the problem is with Cesiums. Namely, the vdW
>radius of Cesium that is internally stored and used to detect
>bonds is 2.35 Angstrom. This means that there are lots of automatically
>detected Cs-Cs bonds and enormous number of torsions.
>The workaround would be to use smaller value as Cs vdW
>radius, however there is no way to change the internally
>stored value at present.
>Regards,
>Alex Granovsky