RE: colvar restraint simulation

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Feb 25 2019 - 11:35:05 CST

This looks mostly ok. What happens when you try to run it? The logfile will tell you exactly what will be done if you read through it.

-Josh

On 2019-02-25 10:10:48-07:00 owner-namd-l_at_ks.uiuc.edu wrote:

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.

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