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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="stopSpelling">> Date: Thu, 27 Mar 2008 12:59:06 -0700<br>> From: dmobley@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] minimization -- bugzilla or general advice?<br>> <br>> Berk,<br>> <br>> > I assume you are using a rigid water model, and thus constraints via SETTLE.<br>> <br>> Yes, OK.<br>> <br>> > Constraining is required to measure the size of the force (for convergence<br>> > and<br>> > step size adjustment) and to make correct steps without enormous extra<br>> > displacements in the direction of the force which could cause problems due<br>> > to non-linearity.<br>> > In Gromacs 3 we had only a coordinate version of SETTLE and LINCS<br>> > did not work well for "triangle constraints". So to constrain the force<br>> > during EM<br>> > we needed to use only coordinates. The trick is to add c*f to the<br>> > coordinates,<br>> > somewhat analogous to constraining velocities in leap frog, and then get the<br>> > force without constraint components as:<br>> > (x+c*f - constrained(x+c*f))/c<br>> > I chose c as the minimization step size divided by the maximum force.<br>> > But there are two issues here, for large c non-linearity problems<br>> > and for small c float/double accuracy issues.<br>> > The non-linearity issue could be causing your problems.<br>> <br>> > Although there is also another issue: water is difficult to minimize in<br>> > general.<br>> <br>> Hmm. Is this different from how other packages handle this issue? I<br>> have never had the recurring problems with minimization in GROMACS<br>> that I have in other packages. Even though, strangely enough, water is<br>> a common feature in most of the simulations I run.<br>> <br>> I'll try and give this a shot in GROMACS 4 soon, I suppose. And I'll<br>> put together a bugzilla.<br>> <br>> Thanks,<br>> David<br><br>I would guess other packages would use a RATTLE like constraint algorithm,<br>both for water and other molecules.<br>So this could be the source of the problem.<br>But please try 4.0 before submitting a bugzilla and speculating further.<br><br>Berk.<br><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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