collective variable restraint

Sun Tao taosun... at gmail.com
Mon Mar 6 00:29:59 CET 2017


Dear All:

I am trying to do umbrella sampling for a system. My collective variable is 
defined as a linear combination of the z-coordinates of some atoms, as the 
following:

        FUNCTION 
CV8+CV9+CV10+CV11+CV12+CV13+CV14+CV15+CV16+CV17+CV18+CV19+CV20+CV21+CV22-2*CV1-2*CV2-2*CV3-2*CV4-2*CV5-2*CV6-2*CV7
        VARIABLES CV1 CV2 CV3 CV4 CV5 CV6 CV7 CV8 CV9 CV10 CV11 CV12 CV13 
CV14 CV15 CV16 CV17 CV18 CV19 CV20 CV21 CV22 
        ERROR_LIMIT 1.0E-8

and add one harmonic potential to the defined collective variable:

 &CONSTRAINT
  &COLLECTIVE
    TARGET [bohr] 40.0
    INTERMOLECULAR .TRUE.
    COLVAR 1
    &RESTRAINT
      K [kcalmol] 10.0
    &END
  &END COLLECTIVE
 &END CONSTRAINT

Somehow the simulation failed with "CPASSERT failed" information, and by 
checking the trajectory, I find many atoms are flying away out of scope. I 
guess this is due to  "INTERMOLECULAR .TRUE." statement? Shall I include 
all the atoms involved in the collective variable into a defined molecule 
in the input file? The input files are attached in the information. Please 
take a look and any feedback would definitely help me to figure it out.

Thank very much !

Tao
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