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Hi,<br><br>Maybe there is an older grompp in your path.<br>Type grompp -h to see which version you are using.<br>And:<br>which grompp<br>to see where it comes from.<br><br>Berk<br><br>> Date: Mon, 11 May 2009 13:03:07 +0300<br>> From: neamtuandrei@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull code problem<br>> <br>> Hi Berk,<br>> thank you for the reply<br>> <br>> here is my mdp file:<br>> <br>> ;<br>> <br>> ; User aneamtu <br>> <br>> ; Joi, 7 mai - 2009<br>> <br>> ; Input file<br>> <br>> ;<br>> <br>> title = Production_runs<br>> <br>> ;define = -DPOSRES -DPOSRES_CA2+_IONS<br>> <br>> <br>> <br>> ;constraints = all-bonds<br>> <br>> <br>> <br>> integrator = md<br>> <br>> dt = 0.001 <br>> <br>> nsteps = 50000 <br>> <br>> <br>> <br>> nstcomm = 1<br>> <br>> nstxout = 1000<br>> <br>> nstvout = 1000<br>> <br>> nstfout = 1000<br>> <br>> nstlog = 500<br>> nstxtcout = 50<br>> xtc_grps = Protein_ions<br>> <br>> <br>> nstenergy = 100<br>> <br>> nstlist = 10<br>> <br>> ns_type = grid<br>> <br>> <br>> coulombtype = PME<br>> <br>> rlist = 1.0<br>> <br>> rcoulomb = 1.0<br>> <br>> rvdw = 1.0<br>> optimize_fft = yes<br>> <br>> <br>> Tcoupl = v-rescale<br>> <br>> tc-grps = Protein SOL ions<br>> <br>> tau_t = 0.1 0.1 0.1<br>> <br>> ref_t = 310 310 310<br>> <br>> <br>> <br>> energygrps = Protein SOL CA2+ NA+ CL-<br>> <br>> <br>> <br>> Pcoupl = berendsen<br>> <br>> Pcoupltype = isotropic<br>> <br>> tau_p = 0.5<br>> <br>> compressibility = 4.5e-5<br>> <br>> ref_p = 1.0<br>> <br>> <br>> <br>> gen_vel = no<br>> <br>> gen_temp = 310.0<br>> <br>> gen_seed = 173529<br>> <br>> <br>> <br>> pull = constraint<br>> pull_geometry = distance<br>> pull_dim = Y Y Y<br>> pull_nstxout = 10<br>> pull_nstfout = 10<br>> pull_ngroups = 2<br>> pull_group0 = Protein<br>> <br>> pull_group1 = CA2+1<br>> pull_rate1 = 0.3<br>> <br>> pull_group2 = CA2+2<br>> pull_rate2 = 0.3<br>> <br>> <br>> I do not understand what I do wrong..<br>> Should I use a -pi pull.ppa file like in gromacs 3.x ?<br>> <br>> Andrei<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />What can you do with the new Windows Live? <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>Find out</a></body>
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