[gmx-users] Re: Using virtual site
라지브간디
rajiv at kaist.ac.kr
Wed May 1 15:16:41 CEST 2013
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
~
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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