Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from both groups.
Srinivs. On Thu, Mar 18, 2010 at 4:55 PM, Zuzana Benkova <zuzana.benk...@savba.sk>wrote: > Dear GROMACS users, > I have checked the mails in archive which deal with the problem I am facing > but did not find the answer what I do wrong. > > I want to compile a PEO chain centered in box of 2900 water molecules. > > In my md.mdp the relevant section is as follows > Tcoupl = nose-hoover > tc-grps = PEO SOL > tau_t = 0.1 0.1 > ref_t = 50 50 > gen_vel = yes > gen_temp = 50 50 > > I have generated an index file where I have defined the PEO group. The [ > SOL ] group contains 129-8828 atoms and the [ PEO ] contains 1-128atoms. > This matches with the gro file. I tried to prepare a tpr file using > > grompp -f md.mdp -c PEO18_2900TIP3P_opt.gro -n PEO18_2900TIP3P.ndx -p > topol.top -o PEO18_2900TIP3P_50K > > and got message > > Program grompp, VERSION 4.0.3 > Source code file: readir.c, line: 1050 > > Fatal error: > 16 atoms are not part of any of the T-Coupling groups > > I tried the compilations with 4.0.3 and 4.0.5 versions but the message was > the same. > > > I would be really thankful for an advice which can move me further. Thank > you in advance. > > Zuzana > > > > > -- > 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/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/mailing_lists/users.php > -- ********************************************* J. Srinivasa Rao Ph.D. Post-doctoral Research Associate C/o Prof. Luis R Cruz Cruz Computational Biophysics Group Department of Physics Drexel University 3141 Chestnut St Philadelphia, PA 19104, USA. Ph: Off: 215-895-1989 Mob: 704-706-4191 Web:http://jsrao.web.officelive.com/default.aspx **********************************************
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