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

[Kenji Mochizuki]

Dear EB

Thank you very much. 
Now, it works and looks OK to me. 

Regards

Kenji

----- Original Message -----
>> From: Emanuel Birru <Emanuel.Birru at monash.edu>
>> To: 'Discussion list for GROMACS users' <gmx-users at gromacs.org>
>> Date: 2013-01-28 14:04:37
>> Subject: RE: [gmx-users] making .top file of new LJ in Water
>> 
>> 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
>> 
>> Cheers,
>> EB
>> -----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 ?
>> 
>> Regards
>> 
>> 
>> === 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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>> 

====================
National Institutes of Natural Sciences
  Institute for Molecular Science

  Kenji Mochizuki

  e-mail: kmochi at ims.ac.jp
  phone: 0564-55-7394
====================