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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Mon, 20 Oct 2008 23:27:38 +0800<br>> From: liyang1980_0_0@163.com<br>> To: gmx-users@gromacs.org<br>> Subject: RE: RE: [gmx-users] how to set pull code in gmx 4<br>> <br>> <br>> Hi Berk<br>> <br>> Thanks for your reply<br>> <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>> Sorry for my poor expression.<br>> <br>> Take a example, In gmx 3.3, the pull dimension and position can be <br>> writen as:<br>> "pull_type = umbrella ; umbrella sampling<br>> pull_dim = N N Y ; pulling performed in Z dimension<br>> pos1 = 0 0 1" ; the reference distance in Z dimension is 1nm<br>> <br>> In gmx 4, for "pull_init1 = 1", which dimension of the reference <br>> distance does it mean ？<
br>> Or say, there is still a single pulling performed in one dimension, like <br>> gmx 3.3, and when setting "pull_dim = N N Y", the "pull init1=1" means <br>> the reference distance in Z dimension is 1nm; while "pull_dim=Y N N" <br>> means the reference distance in X dimension is 1nm？<br>> <br>> Maybe my thinking sounds stupid, I don't know.<br>> Waiting for your reply.<br>> <br>> Li Yang<br><br>You chose pulling distance, so you pull along the distance vector between<br>groups 0 and 1. Since you choose pull_dim= N N Y, the distance is only<br>taken along Z. pull_init1=1 means a (starting) distance of 1.<br>So a distance of 1 nm in z. Note that group 1 could be 1 nm above OR below group 0.<br><br>Another (nearly indentical) setup would be:<br>pull_geometry = direction<br>pull_vec = 0 0 1<br>pull_init = 1<br>This would mean that group 1 is 1 nm above group 0.<br>In this case pull_dim is irrelevant, as long as z is Y.<br><br>Berk.<br><br><br
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