[gmx-users] simulating liquid SO2 (Sulphur dioxide)

[Marcelo Depólo]

Em 05/04/2015 14:44, "Jashimuddin Ashraf" <jashimuddin.ashraf23 at gmail.com>
escreveu:
>
> Dear gromacs users,
>
> I am trying to simulate liquid SO2 (Sulphur dioxide). So I tried to create
> an equilibrated structure of SO2 molecules using the gmx insert-molecules
> function. As I try to minimize the energy of the system, I always get
this-
>
>
------------------------------------------------------------------------------------------------------------------------
> Energy minimization has stopped, but the forces have not converged to the
> requested precision Fmax < 10 (which may not be possible for your system).
> It
> stopped because the algorithm tried to make a new step whose size was too
> small, or there was no change in the energy since last step. Either way,
we
> regard the minimization as converged to within the available machine
> precision, given your starting configuration and EM parameters.

That isn't necessarily a problem here, unless the maximum force is too
high. You have requested a low threshold (emtol =10) and the machine
precision can't reach it on simple precision.

>
------------------------------------------------------------------------------------------------------------------------
>
> I tried to analyze my .gro file that the gmx insert-molecules function is
> returning me and found that some of my SO2 have a bond in between them. Is
> this what causes the energy minimization to crash?

Also, the .gro file just outputs atoms coordinates. There is no 'bonds' on
it. Usualy, that is a visualization problem.

Is there any way I can
> prepare an equilibrated system of liquid SO2 ?

Yes. Read the paper 'Force field benchmark for organic liquids' and you
might get an idea how to do it.

>
> My SO2.itp file is like this (I made this an .itp because I wish to study
> this system along with some other molecules)-
>
>
------------------------------------------------------------------------------------------------------------------------
>
> [ moleculetype ]
> ; Name                   nrexcl
> SO2                    3
>
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass
> typeB    chargeB      massB
>
>      1      opls_202      1     SR      S      1     0.6512      32.07
> ;qtot 0.6512
>      2      opls_326      1     SR     O1      2    -0.3256      15.99940
> ;qtot 0.3256
>      3      opls_326      1     SR     O2      3    -0.3256      15.99940
> ; qtot 0
>
>
> ; opls_202   S   16   32.07     0.6512         A    3.61500e-01  1.2125232
> ; opls_326   O   8   15.99940    -0.3256      A    3.00500e-01  0.47756176
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1         0.1434     635968.0
>     1     3     1      0.1434    635968.0
>
> [ distance_restraints ]
> ;  ai    aj type index type' low up1 up2 fac
>    1     2     1     0      1   1.149  1.490  1.490  1.0
>    1     3     1     0      1   1.149  1.490  1.490  1.0
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1
> c2            c3
>     2     1     3     1        119.5        1359.8
>
------------------------------------------------------------------------------------------------------------------------
>
> I have also uploaded the .gro file that the gmx insert-molecules function
> is returning me after this text.
> ​
>  SO2_box300.gro
> <
https://docs.google.com/file/d/0B8p1k0KkNddyUEN3dzZRZE5keXM/edit?usp=drive_web
>
> ​
> Thanks in advance.
> --
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