Thanks! The problem was indeed the spaces in the group names. Vaithee ======================================================= S. Vaitheeswaran Post-doctoral Research Associate Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute 110 8th Street, Troy NY 12180 Tel: 518-276-4245 email: vai...@rpi.edu =======================================================
On Fri, May 8, 2009 at 4:53 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > S. Vaitheeswaran wrote: > >> Dear gromacs users, >> >> I am trying to calculate the PMF along the end-to-end distance for a short >> polymer (hexa-ethylene glycol), using the pull code in gromacs-4.0.4. I run >> grompp with: grompp_s -v -n OH_ends.ndx -f sd.mdp -c 0.425nm.pdb -p 6EG.top, >> where sd.mdp is: >> ************************ >> title = cpp = /usr/bin/cpp >> integrator = sd >> dt = 0.002 ; [ps] >> nsteps = 1000000 >> nstcomm = 10 ; frequency for center of mass motion >> removal >> comm_mode = Linear ; Remove center of mass translation >> comm_grps = system >> nstxtcout = 10000 ; frequency to write coordinates to xtc >> trajectory >> nstxout = 10000 ; frequency to write coordinates to output >> trajectory file >> nstvout = 100000 >> nstlog = 10000 >> nstenergy = 10000 >> energygrps = 6EG ; group(s) to write to energy file >> pbc = no >> nstlist = 0 ; neighbor list is only constructed once and >> never updated. >> ns_type = simple >> rlist = 0 ; cut-off distance for the short-range >> neighbor list >> rcoulomb = 0 >> rvdw = 0 >> tc-grps = 6EG >> tau_t = 0.1 ; [ps] >> ref_t = 300 ; [K] >> pull = umbrella >> pull_geometry = distance >> pull_init1 = 0.425 ; [nm] >> pull_dim = Y Y Y >> pull_ngroups = 1 >> pull_group0 = group 1 >> pull_group1 = group 2 >> pull_k1 = 1000 >> ************************ >> group 1 and group 2 are defined in OH_ends.ndx: >> ************************ >> [ group 1 ] >> 1 2 >> [ group 2 ] >> 20 21 >> ************************ >> >> and 6EG.top is: >> ************************ >> #include "ffgmx.itp" >> #include "6EG.itp" >> [ system ] >> Hexa-ethylene glycol: Langevin dynamics >> [ molecules ] >> 6EG 1 >> ************************ >> >> But, grompp fails with: >> ------------------------------------------------------- >> Program grompp_s, VERSION 4.0.4 >> Source code file: readir.c, line: 1013 >> >> Fatal error: >> Group 6EG not found in indexfile. >> Maybe you have non-default goups in your mdp file, while not using the >> '-n' option of grompp. >> In that case use the '-n' option. >> ------------------------------------------------------- >> >> But, I *am* using the -n option! If I include the group 6EG in the index >> file (I didn't think it was necessary since it is defined in the .top file), >> grompp chokes with: >> "Fatal error: Group group 1 not found in indexfile.", even though group 1 >> is defined in the .ndx file. >> > > Perhaps try taking the spaces out of the group names, i.e., group_1 and > group_2. > > -Justin > > It works fine without the pulling options. I have searched the manual, >> wiki and mailing list archives for a solution, without success. This >> gromacs newbie is out of ideas -- any help is much appreciated. >> >> thanks, >> Vaithee >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.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 >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > >
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