[gmx-users] making .top file of new LJ in Water

Kenji Mochizuki kmochi at ims.ac.jp
Mon Jan 28 05:45:39 CET 2013

Dear gmx users

I would like to start MD simulation for GAS Hydrate, 
consisting of TIP4P and LJ representing N2.

I have made .top file by hand as following. 
When I use grompp_d for making .tpr file, 
I got the following error.

However, LJ name in .gro file is same as in .top file, which is "NX"
I am not sure what is wrong.

Could you please give me some advise ?


=== error ===
WARNING 1 [file GAS_Hydrate.top, line 25]:
  4353 non-matching atom names
  atom names from GAS_Hydrate.top will be used
  atom names from N1088-N2.gro will be ignored

=== .top file ====

#include "ffoplsaa.itp"
;----Nitrogen Molecule---------
[ atomtypes ]
NX           NX      0.0000  0.0000  A   3.69800e-01  0.787014e+00
[ moleculetype ]
LJN             3
[ atoms ]
     1         NX      1    LJN     NX       1    0.00000  28.000000

;--- TIP4P --
#include "tip4p.itp"

[ system ]
GAS Hydrate

[ molecules ]
LJN      1
SOL   1088

Kenji Mochizuki

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