-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi and thank you for your answer,
Unfortunately, it didn't help. I'm wondering if the reason is that the structure file from which I do the index and would like to use for the md is in 'pdb' format. This structure file comes from a previous mdrun where I performed an energy minimization. To test this hypothesis I converted this structure file to 'gro' format using editconf, simply: editconf -f after_em.pdb -o after_em.gro and then tried to make the index file again from the latter file. It didn't work either. But I thought the problem might be in the 'pdb' structure file produced by mdrun. Could this happen? Cheers, Miguel MGiò wrote: > Hi Miguel! > the same thing happened to me just yesterday. My problem was that, for > some reasons not worth to tell, some atoms were missing from one of my > groups. I made a new index.ndx file and no errors were reported anymore. > So my piece of advice is check your index file. I hope it helps, > greetings, > MGiò > > > On 3/7/06, *Miguel Ortiz Lombardia* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Hi all, > > I get this error from grompp: > > Program grompp, VERSION 3.3 > Source code file: readir.c, line: 1131 > > Fatal error: > Not enough ref_t and tau_t values! > > However, I do have three values for ref_t and tau_t, as many as groups > (I made an index.ndx file that I feed to grompp to support the > non-standard group ('Na') > > This is my input: > > > title = 20ps Position-restrained MD > cpp = /lib/cpp -traditional > define = -DPOSREF > integrator = md > dt = 0.002 > nsteps = 10000 > nstxout = 1000 > nstvout = 1000 > nstlog = 1000 > nstenergy = 50 > nstxtcout = 50 > xtc_grps = Protein > energygrps = Protein SOL Na > nstlist = 10 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 0.9 > tcoupl = Berendsen > tc-grps = Protein SOL Na > tau_t = 0.1 0.1 0.1 > ref_t = 300 300 300 > Pcoupl = Berendsen > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > gen_vel = yes > gen_temp = 300 > gen_seed = 173529 > constraints = all-bonds > > > Any clues? > > > Cheers, > > > Miguel > -- > Miguel Ortiz Lombardía > Centro de Investigaciones Oncológicas > C/ Melchor Fernández Almagro, 3 > 28029 Madrid, Spain > Tel. +34 912 246 900 > Fax. +34 912 246 976 > email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > www: http://www.ysbl.york.ac.uk/~mol/ > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Je suis de la mauvaise herbe, > Braves gens, braves gens, > Je pousse en liberté > Dans les jardins mal fréquentés! > Georges Brassens _______________________________________________ gmx-users mailing list [email protected] <mailto:[email protected]> http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>. Can't post? Read http://www.gromacs.org/mailing_lists/users.php <http://www.gromacs.org/mailing_lists/users.php> > ------------------------------------------------------------------------ > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: [EMAIL PROTECTED] www: http://www.ysbl.york.ac.uk/~mol/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Je suis de la mauvaise herbe, Braves gens, braves gens, Je pousse en liberté Dans les jardins mal fréquentés! Georges Brassens -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.1 (GNU/Linux) iD8DBQFEDY+rF6oOrDvhbQIRArBxAJ4ijHdfzP6ldls6BCiqOdF1K0sZ7wCfRFuV BUvoMRLlftTjBlnUL8dE2qA= =D+a6 -----END PGP SIGNATURE----- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
