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Hi,<br><br>Do you have another line with "pull =" somewhere in your mdp file?<br><br>PS You should switch to Gromacs 4.0.4, since it contains several small<br>bug fixes for the pull code.<br><br>Berk<br><br>> Date: Mon, 11 May 2009 12:38:35 +0300<br>> From: neamtuandrei@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull code problem<br>> <br>> hello,<br>> <br>> I am trying to do a pulling simulation with gromacs 4.0.2<br>> <br>> I added the following lines to the .mdp input file for grompp:<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>> <br>> when I run<br>> > grompp -f production_prm.mdp .......etc.<br>> <br>> it does not recognize the keywords for pulling:<br>> <br>> Ignoring obsolete mdp entry 'title'<br>> <br>> Back Off! I just backed up neutr_RCK_Mthk_solv.04.mdout.mdp to<br>> ./#neutr_RCK_Mthk_solv.04.mdout.mdp.6#<br>> <br>> WARNING 1 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_geometry' in parameter file<br>> <br>> WARNING 2 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_dim' in parameter file<br>> <br>> WARNING 3 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_nstxout' in parameter file<br>> <br>> WARNING 4 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_nstfout' in parameter file<br>> <br>> WARNING 5 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_ngroups' in parameter file<br>> <br>> WARNING 6 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_group0' in parameter file<br>> <br>> WARNING 7 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_group1' in parameter file<br>> <br>> WARNING 8 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_rate1' in parameter file<br>> <br>> WARNING 9 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_group2' in parameter file<br>> <br>> WARNING 10 [file production_prm.mdp, line unknown]:<br>> Unknown or double left-hand 'pull_rate2' in parameter file<br>> <br>> .......<br>> <br>> It appears that grompp doesnot recognize any of these keywords...<br>> <br>> Does anybody can help?<br>> <br>> Thank you<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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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