[gmx-users] Re: Using virtual site

[Mark Abraham]

On Wed, May 1, 2013 at 3:16 PM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> Dear
> Mark,
>
>
>
>
> As per you suggestion, I have simulated a single CO as well as
> CO-with-vsite in a box.
>
>
>
>
> A single CO runs without any problem, BUT the CO-with-vsite
> gives an same error as before:
>
>
>
>
> Steepest
> Descents:
>
>    Tolerance (Fmax)   =
>  1.00000e+03
>
>    Number of steps    =
>      50000
>
> Step=    0, Dmax= 1.0e-02 nm, Epot=
> -3.73341e+04 Fmax= 3.38911e+05, atom= 2
>
> Step=    1, Dmax= 1.0e-02 nm, Epot=
> -4.54970e+04 Fmax= 4.95889e+05, atom= 2
>
> Step=    2, Dmax= 1.2e-02 nm, Epot=
> -6.18180e+04 Fmax= 9.34585e+05, atom= 2
>
> Step=    3, Dmax= 1.4e-02 nm, Epot=
> -1.10395e+05 Fmax= 3.03088e+06, atom= 1
>
> Step=    5, Dmax= 8.6e-03 nm, Epot=
> -2.09874e+05 Fmax= 1.09138e+07, atom= 2
>
> Step=    9, Dmax= 1.3e-03 nm, Epot=
> -2.42526e+05 Fmax= 1.45550e+07, atom= 1
>
> Step=   11, Dmax= 7.8e-04 nm, Epot=
> -2.67493e+05 Fmax= 1.76910e+07, atom= 2
>
> Step=   14, Dmax= 2.3e-04 nm, Epot=
> -2.76005e+05 Fmax= 1.88299e+07, atom= 2
>
> Step=   16, Dmax= 1.4e-04 nm, Epot=
> -2.81365e+05 Fmax= 1.95651e+07, atom= 2
>
> Step=   19, Dmax= 4.2e-05 nm, Epot=
> -2.83032e+05 Fmax= 1.97967e+07, atom= 1
>
> Step=   23, Dmax= 6.3e-06 nm, Epot=
> -2.83281e+05 Fmax= 1.98315e+07, atom= 1
>
> Step=   26, Dmax= 1.9e-06 nm, Epot=
> -2.83355e+05 Fmax= 1.98418e+07, atom= 2
>
> Step=   28, Dmax= 1.1e-06 nm, Epot=
>        nan Fmax= 0.00000e+00, atom= 0
>
> 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.
>
>
>
>
> writing lowest energy coordinates.
>
>
>
>
> Back Off! I just backed up min.gro to ./#min.gro.1#
>
>
>
>
> Steepest Descents converged to machine precision in
> 29 steps,
>
> but did not reach the requested Fmax < 1000.
>
> Potential Energy  = -2.8335531e+05
>
> Maximum force     =  1.9841798e+07
> on atom 2
>
> Norm of force     =  1.6200760e+07
>
>
>
>
>
>
>
> I am afraid that I am a making any mistakes of setting the
> vsite?
>
>
>
>
>
> My
> topology file vsite setting :
>
>
>
>
> [ moleculetype ]
>
>
> ;
> Name            nrexcl
>
> Other_chain_A       3
>
>
>
> [ atoms ]
>
> ;   nr       type  resnr
> residue  atom   cgnr     charge       mass
>  typeB    chargeB      massB
>
> ; residue 157 CMO rtp CMO  q -1.6
>
>      1
>  C    157    CMO      C
>  1      -0.75     12.011   ; qtot -0.75
>
>      2
>  O    157    CMO      O
>  2      -0.85    15.9994   ; qtot -1.6
>
>      3
>  I     157     CMO      I
>   3       1.6      0.0000
>
> [ bonds ]
>
> ;  ai    aj funct
>        c0            c1
>            c2
>  c3
>
>     1     2     2
>    gb_4
>
> [ virtual_sites2 ]
>
> ; Vsite from        funct
>   a
>
>
>
>
> 3       1     2
>     1       0.4376625
>
>
>
>
>
>
>
> My coordiante (.gro) file where i added the vsite xyz: Also included
> the vsite atom info in atomypes as well as ffnonbonded.itp.
>
>
>
>
> Gravel
> Rubs Often Many Awfully Cauterized Sores
>
>
>   3
>
>
> 157CMO      C    1   1.625   2.697
> 0.490
>
>
> 157CMO      O    2   1.722   2.647
> 0.482
>
>
> 157CMO       I     3   1.673   2.672
>   0.486
>
>  0.09660
>   0.05040   0.00760
>
>
This box is far too small.

Mark


> ~
>
>
>
>
>
>
> Could you tell what mistakes I am making here ?
>
>
>
>
>
> Thanks in advance.
>
>
>
>
>
> Raju
>
>
>
>
>
> On Wed, May 1, 2013 at ��������������� :
>
>
>
> I mean simulate a single CO in a box. Then CO-with-vsite in a box.
> If you
> can do that, then a bunch of problems are known to be solved. Leaping in
> the deep end with a complex system means you don't know where the trouble
> comes from when you have it.
>
> Mark
>
> On Wed, May 1, 2013 at 8:45 AM, ���������������
> <rajiv at kaist.ac.kr> wrote:
>
> > Dear Mark,
> >
> > > You mean do the CO simulation and then add V-site upon
> production run?
> >
> > Could you please more specific, what has to be done to avoid this
> error?
> >
> >  >
> > On Fri, Apr 26, 2013 at 6:16 PM, ������������������������������
> <rajiv at kaist.ac.kr> wrote:
> >
> > 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
> >
>
>
>
> --
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