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