<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Hi,<br><br>pull_pbcatom is indeed a global atom index.<br>I will add this information to the mdp description.<br>I don't see how any atom number would not be affected by reordering your topology,<br>except if you are thinking of group that consist of exactly one molecule.<br><br>But pull_pbcatom does not have to be part of the pull group.<br>Although in most cases user will choose it to be part of the group,<br>one can think of cases where an atom not part of the group is more central.<br>Code wise I don't see any reason why this should not work.<br>Are you sure that this does not work?<br><br>I don't see why you would want pull_pbcatom to take an index group.<br>Apart from the fact that this will complicate the option description and processing,<br>you will have to make an index group with one atom index, which you would<br>otherwise fill in directly in pull_pbcatom.<br><br>Berk<br><br>> Date: Mon, 23 Feb 2009 01:26:12 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull_pbcatom appears global and could benifit from a sanity check during grompp<br>> <br>> Hello,<br>> <br>> I am using the pull code (umbrella, distance) to restrain molecule M <br>> to a specified distance from group G in gromacs 4.0.4. I recently <br>> found that I needed to specify pull_pbcatom(G) and restarted my <br>> simulations using a rationally selected atom from that group. However, <br>> the distance restraint appeared to stop working, even though the <br>> forces output in the .pf.xvg file were large. I am by now pretty sure <br>> that what pull_pbcatom requires is the global atom number (ranging <br>> from 1 to N over the entire .gro file; sensitive to topology <br>> reordering) and not the group-specific atom number (ranging from 1 to <br>> G over the selected group; insensitive to topology reordering). <br>> Actually, I had expected pull_pbcatom to accept a .ndx file group, and <br>> when it didn't then I incorrectly guessed the group-specific numbering <br>> as outlined above.<br>> <br>> First, can anybody confirm this?<br>> <br>> Second, my specified pull_pbcatom0 was not even part of pull_group0 if <br>> indeed the atom numbering is global. I think that there should be a <br>> fatal error generated in this case.<br>> <br>> Third, I suggest the following addition to the online .mdp option text <br>> for the pull code pull_pbcatom:<br>> <br>> Existing:<br>> "The reference atom for the treatment of periodic boundary conditions <br>> inside the group (this has no effect on the treatment of the pbc <br>> between groups). This option is only important when the diameter of <br>> the pull group is larger than half the shortest box vector. For <br>> determining the COM, all atoms in the group are put at their periodic <br>> image which is closest to pull_pbcatom1. A value of 0 means that the <br>> middle atom (number wise) is used."<br>> <br>> To Add:<br>> "When pull_pbcatom is greater than zero, the atom number is treated <br>> globally and should therefore correspond to the atom number in the <br>> .gro file as it would in an index file group. Hence, pull_pbcatom is <br>> sensitive to a reordering of your topology"<br>> <br>> Fourth, for the long term development I suggest that this should be <br>> supplied as a .ndx file group.<br>> <br>> Thanks,<br>> Chris.<br>> <br>> <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 />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
</html>