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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>Have you looked at the mdp options help in the pdf or html manual?<br>The html manual is not online yet for 4.0, but you can find it in your Gromacs<br>directory at: share/html/online/mdp_opt.html<br></div><br>If you use pull_geometry=distance you need to set the reference distance,<br>which would be (assuming you want 1 nm):<br>pull_init1 = 1<br><br>Berk<br><br><br><hr id="stopSpelling">> Date: Sat, 18 Oct 2008 22:45:38 +0800<br>> From: liyang1980_0_0@163.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] how to set pull code in gmx 4<br>> <br>> Dear all<br>> <br>> I cannot understand the explanations about settings of pull code in the<br>> gmx 4.<br>> <br>> Take a example, there are two particles in the system, and I want to<br>> reproduce the LJ potential using "umbrella sampling".<br>> The settings in gmx 3.3.3 is following:<br>> =====================<br>> ..........<br>> runtype = umbrella<br>> ngroups = 1<br>> group_1 = Arg2<br>> reference_group = Arg1<br>> ......<br>> pulldim = N N Y<br>> K1 = 700<br>> POS1 = 0 0 1<br>> ======================<br>> <br>> But I don't know how to set it in gmx 4<br>> Following is the settings in gmx 4:<br>> ======================<br>> ; COM PULLING<br>> ; Pull type: no, umbrella, constraint or constant_force<br>> pull = umbrella ; ---> "runtype" in gmx 3.3.3<br>> ; Pull geometry: distance, direction, cylinder or position<br>> pull_geometry = distance<br>> ; Select components for the pull vector. default: Y Y Y<br>> pull_dim = N N Y ; ---> "pulldim" in gmx 3.3.3<br>> ; Cylinder radius for dynamic reaction force groups (nm)<br>> pull_r1 = 1<br>> ; Switch from r1 to r0 in case of dynamic reaction force<br>> pull_r0 = 1.5<br>> pull_constr_tol = 1e-06<br>> pull_start = no<br>> pull_nstxout = 10<br>> pull_nstfout = 1<br>> ; Number of pull groups<br>> pull_ngroups = 1 ; ---> "ngroups" in gmx 3.3.3<br>> ; Group name, weight (default all 1), vector, init, rate (nm/ps),<br>> kJ/(mol*nm^2)<br>> pull_group0 = Arg2 ; ---> "reference_group" in gmx 3.3.3<br>> pull_weights0 =<br>> pull_pbcatom0 = 0<br>> pull_group1 = Arg1 ; ---> "group1" in gmx 3.3.3<br>> pull_weights1 =<br>> pull_pbcatom1 = 0<br>> pull_vec1 = 0.0 0.0 0.0<br>> pull_init1 = 0.0<br>> pull_rate1 = 0<br>> pull_k1 = 700 ; ---> "k1" in gmx 3.3.3<br>> pull_kB1 = 0<br>> ======================<br>> if right, which parameter corresponds with "pos1" in gmx3.3.3?<br>> <br>> I must apologize in advance if I miss some details in the manual.<br>> <br>> Thank you very much<br>> <br>> Li Yang<br>> <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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