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

Emanuel Birru Emanuel.Birru at monash.edu
Mon Jan 28 06:04:37 CET 2013

Hi Kenji, 

I guess if you change/swap the order of molecules in top file it will work. The order of molecules in your gro file should match up with your top file. If you give us more info it would be good :) I am just guessing :(

[ molecules ]
SOL   1088
LJN      1

Swap them like this

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Kenji Mochizuki
Sent: Monday, 28 January 2013 3:46 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] making .top file of new LJ in Water

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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