[gmx-users] Re: Using virtual site
Richard Broadbent
richard.broadbent09 at imperial.ac.uk
Wed May 1 16:13:49 CEST 2013
Dear Raju,
You haven't added any exclusions to your topology. Therefore, the mid
point is interacting via the coulomb potential with the Carbon and
Oxygen atoms.
If you exclude those interactions this system will probably run.
Richard
On 01/05/13 14:16, 라지브간디 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
>
> ~
>
>
>
>
>
>
> 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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