Dear EB Thank you very much. Now, it works and looks OK to me.
Regards Kenji ----- Original Message ----- >> From: Emanuel Birru <emanuel.bi...@monash.edu> >> To: 'Discussion list for GROMACS users' <gmx-users@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] >> On Behalf Of Kenji Mochizuki >> Sent: Monday, 28 January 2013 3:46 PM >> To: gmx-users@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 >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> ==================== National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 ==================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
