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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>The simple answer is: NEVER EVER do simulation with -DFLEXIBLE for water.<br>The results will be nonsense, as the standard water models have only been parametrized<br>with rigid bonds and angles.<br><br>The only use for this option used to be energy minimization.<br>But as of Gromacs 4.0, all minimizers work with constraints,<br>so now you really never need -DFLEXIBLE.<br><br>Berk<br></div><br><br><br><hr id="stopSpelling">> Date: Fri, 31 Oct 2008 00:26:30 -0400<br>> From: chris.neale@utoronto.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] DFLEXIBLE parameter<br>> <br>> define = -DFLEXIBLE will affect your run most definitely. Exactly how <br>> it will affect your run is, to my knowledge, not yet published. The <br>> common assumption is that it does not matter at all when you are <br>> interested in the solute, which most of us are. To include this <br>> parameter is to allow the O-H bond in many water models to vibrate, as <br>> opposed to being constrained to a constant equilibrium distance. <br>> However, most users desire a computationally faster run utilizing <br>> constraints = all-bonds and a timestep of 2 fs, or constraints = <br>> h-bonds and a timestep of 1 fs, versus constraints = none and define = <br>> -DFLEXIBLE that requires a timestep of 0.5 fs.<br>> <br>> Note that it does not appear to affect all water models (e.g. tip5p)<br>> <br>> The 4.0 manual makes an interesting argument that all bond vibrations <br>> are very much quantum characteristics and are thus equally well <br>> represented by a constraint as they are by a harmonic restraint.<br>> <br>> That's a rambling response, I know, but you need to focus your <br>> question more tightly or include more relevant information if you want <br>> something more direct for an answer.<br>> <br>> Chris.<br>> <br>> -- original message --<br>> <br>> Dear all gmx users and developers,<br>> <br>> Parameter -DFLEXIBLE in mdp file will include flexible water in stead <br>> of rigid water into the topology.<br>> So, will it affect the MD simulation if I include this parameter in <br>> the MD simulation? because it is unnecessary in the run parameter.<br>> <br>> Any comments and suggestions will be well appreciated.<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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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