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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 06:41:12 -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>> > The problem could be in the constraints.<br>> > Gromacs 3 constrains the forces during EM by adding c*f to the coordinates,<br>> > constraining those and then dividing the constraint displacement by c.<br>> > This limits the accuracy.<br>> ><br>> > In Gromacs 4 I have implemented force constraining for LINCS and SETTLE.<br>> > This seems to improve the accuracy a lot.<br>> <br>> I'm running without constraints. Can you explain in a little more<br>> detail what you mean here? c*f, where c is what? Why is this done? I<br>> know "to constrain the forces" but it's not clear to me what the<br>> incentive is.<br><br>I assume you are using a rigid water model, and thus constraints via SETTLE.<br><br>Constraining is required to measure the size of the force (for convergence 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 during EM<br>we needed to use only coordinates. The trick is to add c*f to the 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 general.<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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