colvar restraint simulation

From: Prabir Khatua (prabir07chem_at_gmail.com)
Date: Mon Feb 25 2019 - 11:04:33 CST

Hi NAMD users,

I want to do a distance restraint simulation where I need to use different
force constants
for different distance variables. I am using the following configuration
file

colvar {
  name d1
  distance {
   group1 { atomNumbers 3608} # A6 I31:O
   group2 { atomNumbers 566} # A1 V39:N

  }
}

colvar {
  name d2
  distance {
   group1 { atomNumbers 2462}
   group2 { atomNumbers 2963}

  }
}

colvar {
  name d3
  distance {
   group1 { atomNumbers 2439}
   group2 { atomNumbers 3106}

  }
}

harmonic {
        colvars d1 d2
        centers 3.5 3.5
       force constant 5.0
}

harmonic{
      colvars d3
      centers 4.0
     force constant 1.0
}

I am wondering whether simulation will apply a force constant of 5.0 on d1
and d2, while
1.0 on d3. Please let me know if I am doing wrong and suggest me how to do
it.
Any suggestion would be appreciated.

Thanks,

Prabir

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*

This archive was generated by hypermail 2.1.6 : Sat Dec 07 2019 - 23:20:28 CST