[gmx-users] LINCS warning during energy minimization of nitrogen with virtual site

[Ali Ahmed]

Hello GROMACS users,

I'm doing MD for nitrogen, and for better electrostatic interactions I need
to use massless and charged virtual site. I did that but when I try to do
energy minimization gives me LINCS warning and crush. I don't know where is
the error I tried a lot but could not find a solution.
Anyone has an idea where is my error

Here is the topology file (hand written)

------------------

[ defaults ]

1 3 yes 0.5 0.5

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ atomtypes ]

; name  bond_type    mass    charge   ptype          sigma      epsilon

  OP   OP            0.000   0.000    A              0.330      0.3062 ;
nitrogen

  M      M              0.000   0.000    V              0.000      0.000 ;
virtual site

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ moleculetype ]

; name  nrexcl

N2     2



[ atoms ]

;   nr       type    resnr residue  atom   cgnr   charge     mass

     1     OP      1    N2     N1      1    -0.482          14.0067

     2     M         1    N2     M1      1     0.964         0.000

     3     OP       1    N2     N2      1    -0.482         14.0067



[ constraints ]

; the N-N is fixed

    1   3   1   0.11



[ virtual_sites2 ]

; site  ai  aj  funct   a

     2   1   3      1   0.5000  ; right in the mid



;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

[ system ]

N2 in vacuo



[ molecules ]

N2     1500

------------------------------------------------------------
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Here is the structure (N2.pdb)

-----------

TITLE     N2 with dummy masses

REMARK    THIS IS A SIMULATION BOX

MODEL        1

COMPND    UNNAMED

AUTHOR    GENERATED BY OPEN BABEL 2.3.2

CRYST1   50.000   50.000   50.000  90.00  90.00  90.00 P 1         1

ATOM      1  N1  N2      1       0.000   0.000   0.000  1.00
0.00           N

ATOM      2  M1  N2      1       0.55000   0.000   0.000  1.00
0.00          Xx

ATOM      3  N2  N2      1       1.100   0.000   0.000  1.00
0.00           N

CONECT    1    3

CONECT    3    1

MASTER        0    0    0    0    0    0    0    0    3    0    3    0

END0

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Thank you