<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>I think you mis-read the manual.<br>With constant-force there is no reference position (since a linear potential has no reference point),<br>but you can, and in your case should, use a reference group.<br>Then you can also use the geometry distance.<br><br>Berk<br><br>> Date: Wed, 18 Nov 2009 19:08:43 +0100<br>> From: schlesi@uni-mainz.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] constant_force pulling<br>> <br>> Hi all,<br>> i tried out the constant_force pulling, to simulate a force clamp <br>> pulling experiment. But there are now some questions. But first describe <br>> the system and so on...<br>> The system consists of two molecules which can bind through hydrogen <br>> bonds with no water. Each molecule has one atom which will be consibered <br>> for the pulling. ZUG is that from the molecule that should be pulled and <br>> REF is the one from the other molecule (in umbrella pulling it would be <br>> the reference group). So the system looks the following<br>> REF----hbonds-----ZUG -> pulling in this direction.<br>> <br>> In the *.mdp file i had the following parameters:<br>> pull = constant_force<br>> pull_geometry = direction<br>> pull_dim = Y Y Y<br>> pull_ngroups = 1<br>> pull_group1 = ZUG<br>> pull_k1 = -500<br>> pull_vec1 = 1.631 0.196 0.279<br>> <br>> where pull_vec1 is the vector from REF to ZUG.<br>> The manual states that for constant_force there is no reference group, <br>> so i took for pull_geometry direction, because it looks like that all <br>> the other options need a reference group.<br>> <br>> grompp complained that the pulling is in absolute coordinates and that <br>> this can lead to artefacts (i think when the molecule starts to rotate). <br>> In the end both molecule were pulled together through space, because REF <br>> wasn't fixed (so the molecule could move freely).<br>> <br>> Then i fixed the position of REF via position restraints and a freeze <br>> group (not both together, were two simulations). In both cases grompp <br>> didn't complain about the pulling in absolute coordinates. (I fixed the <br>> position of REF, because that's the same what the pullcode does in <br>> umbrella/position pulling with the reference group, the spring moves <br>> relative to the reference group so the reference group is fixed for the <br>> pulling).<br>> <br>> So now to my questions:<br>> <br>> 1) Would this (to fix the position of REF) be the right way to simulate <br>> a force clamp experiment?<br>> <br>> 2) If so, what would be better for fixing freeze group or position <br>> restraint? I tend to the former because then REF is fixed totally, in <br>> the later cases the two molecule would move a little bit, till the force <br>> from the pulling and restraint will be equilibrated and then i have <br>> nearly the same case as in the freeze group, but REF could fluctuate in <br>> space (how much depends on the strength of the restraints, but i think <br>> it would not be very much).<br>> <br>> 3) What to do with COM? Remove nothing, or only the translation or <br>> translation and rotation? One remark, i disabled the pbc, but i would be <br>> interesed what one should use best without and with pbc (in the later <br>> cases there could be also water present).<br>> <br>> Hope somebody has any ideas.<br>> Greetings<br>> Thomas<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>