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

[Jashimuddin Ashraf]

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-

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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.
------------------------------------------------------------------------------------------------------------------------

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

My SO2.itp file is like this (I made this an .itp because I wish to study
this system along with some other molecules)-

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[ 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
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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.