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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