[gmx-users] lincs warning

[Afsane Farhadi]

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   ----- Forwarded Message ----- From: "Afsane Farhadi" <afsane_farhadi at yahoo.com> To: "gromacs.org_gmx-users at maillist.sys.kth.se" <gromacs.org_gmx-users at maillist.sys.kth.se> Cc:  Sent: Mon, Apr 27, 2020 at 3:52 PM Subject: lincs warning  Hi users I have two types of molecules ,methane and carbondioxide. i optimized them by gaussian calculation and i edited the atom name and residue by vim.  I extracted the epsilon and sigma parameter from the articles . i generated a box of 500 methane molecules and 62 carbondioxide by insert-molecules. I have done energy minimization and its ok (potential energy is  -2e+03).when i was running npt.mdp the lincs warning was showed( bond rotate more than 30 degree)I need help thanks alot for your quick answers .the topology and npt.mdp is:#include "oplsaa.ff/forcefield.itp"

[ atomtypes ]
    CO      C01      12.0110    0.775    A    2.75700E-01   2.33790E-01
    OC      O01      15.99940  -0.388    A    3.03300E-01   6.69120E-01
  opls_801  H801     1.0080     0.125    A    1.48720E-01   0.65688E-01
  opls_803  H803     1.0080     0.125    A    1.48720E-01   0.65688E-01
  opls_804  H804     1.0080     0.125    A    1.48720E-01   0.65688E-01
  opls_800  C800    12.0110    -0.502    A    1.90820E-01   4.57729E-01
  opls_802  H802     1.0080     0.125    A    1.48720E-01   0.65688E-01
[ moleculetype ]
; Name               nrexcl
CH4                   3
[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  
     1   opls_800      1      H   C      1    -0.5020    12.0110 
     2   opls_801      1      H   H      1     0.1250     1.0080 
     3   opls_802      1      H   H      1     0.1250     1.0080 
     4   opls_803      1      H   H      1     0.1250     1.0080 
     5   opls_804      1      H   H      1     0.1250     1.0080 
[ bonds ]
    2     1     1      0.1090 138490.400
    3     1     1      0.1090 138490.400
    4     1     1      0.1090 138490.400
    5     1     1      0.1090 138490.400

[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3 
    2     1     3     1    109.500    146.440
    2     1     4     1    109.500    146.440
    2     1     5     1    109.500    146.440
    3     1     4     1    109.500    146.440
    4     1     5     1    109.500    146.440
    3     1     5     1    109.500    146.440


[ moleculetype ]

; Name               nrexcl
CAR   3

[atoms]

; nr  type resnr residue atom cgnr charge mass

  1   CO    1     CAR    CO   1    0.775  12.0110

  2   OC    1     CAR    OC   1   -0.388  15.9994

  3   OC    1     CAR    OC   1   -0.388  15.9994
  [ bonds ]
  1    2    1   0.11620  844300

  1    3    1   0.11620  844300
  
  
  [angles]
;  ai    aj    ak   funct            c0            c1            c2            c3   

   2     1     3     1           180         451.9
  
  [system]:

co2 in methane


 [molecules]

  CH4     500
  CAR     62################
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