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

[Mark Abraham]

Hi,

No, only mdrun issues LINCS warnings. grompp issues different warnings, and
I would like you to check whether you had any from grompp that you may not
have considered. :-)

Mark

On Tue, Aug 1, 2017 at 5:04 PM Ali Ahmed <aa5635737 at gmail.com> wrote:

> 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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