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Re^2: Why FF with dlc option demands so much of RAM?

Vyacheslav
kreme_vg@chemy.kolasc.net.ru


Hi,
thanks for explanation! Fortunately, I deal with not cesium only…
Best regards,
Vyacheslav
-----------------------------------------------------

On Thu Apr 8 '10 3:10pm, Alex Granovsky wrote
---------------------------------------------
>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


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