<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>You should use pull_geometry=direction.<br>distances don't get negative.<br><br>Berk<br><br>> Date: Sat, 14 Nov 2009 09:21:39 -0500<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] pull code with defined negative relative displacements<br>> <br>> Hello, I am re-running some of our gromacs 3 simulations using gromacs<br>> 4, and as far as I can tell the gromacs 4 pull code, while very nicely<br>> enhanced from gromacs 3, has also lost some functionality.<br>> <br>> I am calculating the PMF of a peptide across a bilayer and, to <br>> simplify the issue, what I can't figure out how to do with gromacs 4 <br>> is to pull group1 to a position 1 nm more negative along the z-axis <br>> than group 0 (the bilayer in this case) for some replicas and to 1 nm <br>> more positive along the z-axis than group 0 in others. I'll focus on <br>> the negative displacement here as it is the one that is giving me <br>> problems.<br>> <br>> This used to be possible with the following gromacs 3 pull.ppa options:<br>> <br>> runtype = umbrella<br>> reftype = com<br>> pulldim = N N Y<br>> reference_group = group0<br>> group_1 = group1<br>> K1 = 500<br>> Pos1 = 0 0 -1.0<br>> <br>> Sure, I could start group1 in the correct negative-z displacement from<br>> group0 and use pull_init1=+1.0, but this will not work when, for<br>> instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),<br>> where the sampling will infrequently jump back and forth about z=0.<br>> <br>> Just to be sure, I tried for gromacs 4 are the following pull code <br>> .mdp options:<br>> <br>> pull = umbrella<br>> pull_geometry = distance<br>> pull_dim = N N Y<br>> pull_start = no<br>> pull_ngroups = 1<br>> pull_group0 = group0<br>> pull_group1 = group1<br>> pull_init1 = -1.0<br>> pull_rate1 = 0<br>> pull_k1 = 500.0<br>> <br>> where mdrun complains:<br>> "Pull reference distance for group 1 is negative (-1.000000)"<br>> <br>> and it is pretty obvious why this doesn't work since it is asking for<br>> a negative displacement. Nevertheless, I tried it and pull_init1<br>> appears to get set to zero.<br>> <br>> I also attempted the following.<br>> <br>> pull = umbrella<br>> pull_geometry = distance<br>> pull_dim = N N Y<br>> pull_start = no<br>> pull_ngroups = 1<br>> pull_group0 = group0<br>> pull_group1 = group1<br>> pull_init1 = 1.0<br>> pull_rate1 = 0<br>> pull_k1 = 500.0<br>> pull_vec1 = 0 0 -1<br>> <br>> where I would then use<br>> pull_init1 = 1.0<br>> pull_vec1 = 0 0 1<br>> for the positive side of the bilayer.<br>> <br>> However, when I look at the forces, I am getting the negative of what <br>> I should get when pull_vec1 = 0 0 -1.<br>> <br>> coord.xvg:<br>> 610.0000 4.9343 -1.02019<br>> 660.0001 4.91454 -0.949747<br>> <br>> force.xvg:<br>> 610.0000 -10.0932<br>> 660.0001 25.1265<br>> <br>> Although I am getting exactly what I should get when pull_vec1 = 0 0 1 <br>> (for intended positive displacements).<br>> <br>> coord.xvg:<br>> 660.0001 4.9014 1.16304<br>> <br>> force.xvg:<br>> 660.0001 -81.5201<br>> <br>> Any ideas are greatly appreciated. I can probably mod the code for my<br>> needs, but a standard gromacs binary is always preferable.<br>> <br>> Thank you,<br>> Chris.<br>> <br>> <br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.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 />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
</html>