<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>This all depends on what you want to achieve.<br>In most cases energy minimization is used to remove atomic overlap from<br>a bad starting structure or from slightly overlapping solvent atoms.<br>If you run your MD with constraints, you probably also want constraints<br>during the (last) minimization step. Otherwise the effects mentioned<br>in the reference you gave might be important.<br><br>Only rarely people are interested in really arriving at the (local) energy minimum.<br>Note that this is only relevant at 0K, which is not the most interesting condition.<br>A notable exception in normal mode analysis, where the method requires<br>a conformation very close to a local minimum.<br><br>Berk<br><br>> Date: Fri, 26 Feb 2010 09:53:02 +0000<br>> From: i.farabella@mail.cryst.bbk.ac.uk<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Constraints and EM<br>> <br>> Dear all,<br>> <br>> I have some doubt regarding energy minimization and the use of<br>> constraint algorithms (such as LINCS) that may come from my<br>> inexperience in GROMACS and molecular dynamics in general.<br>> <br>> In a Berk Hess talk given at the GROMACS workshop 2007 it is stated:<br>> <br>> (https://extras.csc.fi/chem/courses/gmx2007/Berk_talks/forcef.pdf)<br>> <br>> "In GROMACS bonds are usually replaced by constraints, i.e. the<br>> distances between bonded atoms are fixed to their equilibrium value.<br>> Constraints are actually a more faithful representation of reality<br>> since the dynamics of bonds is of quantum nature..”<br>> <br>> In an article about the use of SHAKE (another algorithm for<br>> constraints) I read that:<br>> "Iinitiating a constrained simulation from an unconstrained minimum<br>> usually results in spurious temperature fluctuations that slow down<br>> the equilibration of the molecule and/or introduce artifacts" (Duan,<br>> Y., Kumar, S., Rosenberg, J.M. and Kollman, P.A. "Gradient SHAKE: An<br>> improved method for constrained energy minimization in macromolecular<br>> simulations." Journal of Computational Chemistry (2004), 16(11):<br>> 1351-1356.)<br>> <br>> That suggests to me that the use of constraints during EM is somehow suggested.<br>> However why use constraints (that maintain fixed lengths of the<br>> selected bonds) during this step of the simulation if what you want to<br>> achieve with EM is the local potential energy minimum and it is<br>> required to have a high degree of freedom in the atoms' movement?<br>> <br>> Is my interpretation of the use of constraints wrong?<br>> <br>> Sorry for the long email, any suggestion from an expert point of view<br>> is welcome.<br>> <br>> Thanks<br>> <br>> -- <br>> Irene Farabella<br>> Wellcome Trust PhD student<br>> <br>> Institute of Structural and Molecular Biology<br>> Department of of Biological Sciences<br>> Birkbeck<br>> University of London<br>> Malet Street<br>> London WC1E 7HX<br>> Telephone +44 (0)20 7631 6815<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: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
</html>