From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Mar 11 2015 - 23:17:09 CDT
is there any minimization before starting simulation 2 that might actually
change the value between the end of simulation 1 and the start of 2?
could it perhaps be related to periodic boundary conditions? I'm not sure
exactly how this would manifest, but if the colvar calculation used
non-wrapped coordinates, whereas your output dcd and coor files are
wrapped, that could possibly give different values, and since simulation 2
starts from the coor, it would start from the wrapped condition and look
similar to the dcd analysis (maybe). That all being said, in my past
experience with colvars and dihedrals, everything seemed pretty foolproof
and I recall thinking it handled periodic conditions well, but maybe there
is some option that needs checking.
On Thu, Mar 12, 2015 at 12:05 AM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:
> 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
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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