[gmx-users] Using virtual site

[Mark Abraham]

On Fri, Apr 26, 2013 at 6:16 PM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> Dear gmx,
>
>
> I am having a trouble in setting the virtual site on CO molecule.
>
>
> When I use V-site for CO, it end up with energy minimization error as
> follows:
>
>
>
>
> steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+03
>    Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -3.82767e+05 Fmax= 8.14332e+04, atom=
> 2512
> Step=    1, Dmax= 1.0e-02 nm, Epot= -3.90238e+05 Fmax= 8.68714e+04, atom=
> 2512
> Step=    2, Dmax= 1.2e-02 nm, Epot= -3.97776e+05 Fmax= 1.19106e+05, atom=
> 2512
> Step=    3, Dmax= 1.4e-02 nm, Epot= -4.06486e+05 Fmax= 2.90401e+05, atom=
> 2512
> Step=    4, Dmax= 1.7e-02 nm, Epot= -4.20168e+05 Fmax= 3.68606e+05, atom=
> 2512
> Step=    6, Dmax= 1.0e-02 nm, Epot= -4.22573e+05 Fmax= 3.77163e+05, atom=
> 2511
> Step=    8, Dmax= 6.2e-03 nm, Epot= -4.24217e+05 Fmax= 3.69075e+05, atom=
> 2512
> Step=   10, Dmax= 3.7e-03 nm, Epot= -4.25217e+05 Fmax= 4.81625e+05, atom=
> 2511
> Step=   12, Dmax= 2.2e-03 nm, Epot= -4.25618e+05 Fmax= 3.60189e+05, atom=
> 2512
> Step=   13, Dmax= 2.7e-03 nm, Epot= -4.25861e+05 Fmax= 4.31397e+05, atom=
> 2511
> Step=   15, Dmax= 1.6e-03 nm, Epot= -4.26278e+05 Fmax= 4.18024e+05, atom=
> 2512
> Step=   17, Dmax= 9.7e-04 nm, Epot= -4.26642e+05 Fmax= 4.92899e+05, atom=
> 2511
> Step=   19, Dmax= 5.8e-04 nm, Epot= -4.26741e+05 Fmax= 5.67952e+05, atom=
> 2512
> Step=   21, Dmax= 3.5e-04 nm, Epot= -4.26911e+05 Fmax= 4.14681e+05, atom=
> 2511
> Step=   23, Dmax= 2.1e-04 nm, Epot= -4.27011e+05 Fmax= 5.66533e+05, atom=
> 2512
> Step=   25, Dmax= 1.3e-04 nm, Epot= -4.27043e+05 Fmax= 6.86227e+05, atom=
> 2511
> Step=   27, Dmax= 7.5e-05 nm, Epot= -4.27086e+05 Fmax= 4.56863e+05, atom=
> 2512
> Step=   29, Dmax= 4.5e-05 nm, Epot= -4.27110e+05 Fmax= 4.69971e+05, atom=
> 2511
> Step=   31, Dmax= 2.7e-05 nm, Epot= -4.27126e+05 Fmax= 4.15923e+05, atom=
> 2512
> Step=   32, Dmax= 3.2e-05 nm, Epot= -4.27135e+05 Fmax= 8.56354e+05, atom=
> 2511
> Step=   34, Dmax= 1.9e-05 nm, Epot= -4.27146e+05 Fmax= 5.42283e+05, atom=
> 2512
> Step=   36, Dmax= 1.2e-05 nm, Epot= -4.27152e+05 Fmax= 4.73218e+05, atom=
> 2511
> Step=   37, Dmax= 1.4e-05 nm, Epot= -4.27155e+05 Fmax= 8.62092e+05, atom=
> 2512
> Step=   39, Dmax= 8.4e-06 nm, Epot= -4.27162e+05 Fmax= 4.13479e+05, atom=
> 2511
> Step=   40, Dmax= 1.0e-05 nm, Epot= -4.27164e+05 Fmax= 9.11108e+05, atom=
> 2512
> Step=   42, Dmax= 6.1e-06 nm, Epot= -4.27168e+05 Fmax= 4.89792e+05, atom=
> 2511
> Step=   44, Dmax= 3.6e-06 nm, Epot= -4.27170e+05 Fmax= 4.61416e+05, atom=
> 2512
> Step=   45, Dmax= 4.4e-06 nm, Epot= -4.27171e+05 Fmax= 6.69155e+05, atom=
> 2511
> Step=   47, Dmax= 2.6e-06 nm, Epot= -4.27173e+05 Fmax= 3.68335e+05, atom=
> 2512
> Step=   48, Dmax= 3.1e-06 nm, Epot= -4.27175e+05 Fmax= 4.89636e+05, atom=
> 2511
> Step=   49, Dmax= 3.8e-06 nm, Epot= -4.27175e+05 Fmax= 1.02472e+06, atom=
> 2512
> Step=   51, Dmax= 2.3e-06 nm, Epot= -4.27178e+05 Fmax= 3.60939e+05, atom=
> 2511
> Step=   52, Dmax= 2.7e-06 nm, Epot= -4.27179e+05 Fmax= 5.39389e+05, atom=
> 2512
> Step=   54, Dmax= 1.6e-06 nm, Epot= -4.27180e+05 Fmax= 5.76323e+05, atom=
> 2511
> Step=   55, Dmax= 2.0e-06 nm, Epot= -4.27180e+05 Fmax= 9.58450e+05, atom=
> 2512
> Step=   56, Dmax= 2.3e-06 nm, Epot= -4.27180e+05 Fmax= 1.08106e+06, atom=
> 2511
> Step=   58, Dmax= 1.4e-06 nm, Epot= -4.27182e+05 Fmax= 3.79287e+05, atom=
> 2512
> Step=   59, Dmax= 1.7e-06 nm, Epot= -4.27182e+05 Fmax= 7.55107e+05, atom=
> 2511
> Step=   61, Dmax= 1.0e-06 nm, Epot= -4.27183e+05 Fmax= 4.83668e+05, atom=
> 2512
> Step=   62, Dmax= 1.2e-06 nm, Epot= -4.27183e+05 Fmax= 8.92245e+05, atom=
> 2511
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
>
> writing lowest energy coordinates.
>
>
> Steepest Descents converged to machine precision in 63 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  = -4.2718281e+05
> Maximum force     =  4.8366841e+05 on atom 2512
> Norm of force     =  3.5896956e+03
>
>
>
>
> BUT when i don't use V-site, it doesnt give any error as it runs without
> giving an any errors. I wonder I am making a problem in setting V-site ?
>
>
> i run without using virtual site, its runs without any problem but if use
> virtual site for the ligand it gives this follwing error,
>
>
> I assigned virtual site for CO ligand as like this :
>
>
> [ virtual_sites2 ]
> ; Vsite from                    funct   a
> 2513       2511       2512      1       0.4376625
>
>
> Here, the 2511 is C, 2512 is O and 2513 the dummy (V-site) atom I given. I
> also manually included the V-site xyz coordinates value in .gro file.
>
>
> What i am missing here?.
>

Maybe your starting configuration of atoms is too broken to be useful.
Maybe you have some interaction on atom 2513 that doesn't work.

Make a simple system of CO work, then do CO+vsite. Then apply those lessons
to your complex system.

Mark