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

[Mark Abraham]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>