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

[Ali Ahmed]

Dear Mark
Yes, all the warnings are from grompp.
I have no idea where is the problem in the structure or the topology
Thank you

On Mon, Jul 31, 2017 at 2:34 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Did you get any warnings from grompp?
>
> Mark
>
> On Mon, Jul 31, 2017 at 5:48 PM Ali Ahmed <aa5635737 at gmail.com> wrote:
>
> > 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
> >
> > ------------------------------------------------------------
> > --------------------------------------
> >
> > 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
> >
> > ------------------------------------------------------------
> > ---------------------------------
> > Thank you
> > --
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