Dihedral calculation with colvars

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Mar 11 2015 - 23:05:45 CDT

Dear Users,

I was asking about the dihedral definition in colvars but I soon find out questions more about colvars so I think it might be better to open a new thread. Following is my colvars inputs and basically I want it to calculate the dihedral angle from 4 selections (that I have made into 4 group.pdb) and use a harmonic spring restraining it to certain value:

colvarsTrajFrequency 100
colvarsRestartFrequency 1000

colvar {
   name dih
   width 1.0
   outputValue on

   dihedral {
       group1 {
         atomsFile ../group2.pdb
         atomsCol B
         atomsColValue 1.0
       }
       group2 {
         atomsFile ../group1.pdb
         atomsCol B
         atomsColValue 1.0
       }
       group3 {
         atomsFile ../group3.pdb
         atomsCol B
         atomsColValue 1.0
       }
       group4 {
         atomsFile ../group4.pdb
         atomsCol B
         atomsColValue 1.0
       }
       oneSiteSystemForce yes
   }
   outputSystemForce yes
   outputAppliedForce yes
}

harmonic {
  name diah_pot
  colvars dih
  centers -11.0
  forceConstant 10.0
}

However although it shows perfectly fine inside the colvar.traj, in which the output value under dih is restrained towards the desired value, it is not the case when I use cv plugin in VMD to calculate dihedral (with exactly the same colvars script) for every frame of the dcd. It seems so weird to me.

In addition, when I feed the result coor and vel from this simulation (simulation-1) to the next simulation (simulation-2), the frame 0 of colvar.traj of simulation-2, which suppose to give value of the last frame of simulation-1, however gives the value that VMD cv plugin measures.

I did a number of tests and searches and totally run out of ideas.

Thanks in advance,
Kevin

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