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    On 1/04/2012 5:51 PM, Acoot Brett wrote:
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        <div><span>Hi Mark,</span></div>
        <div><span></span>&nbsp;</div>
        <div><span>Then can you explain in which situation the
            calculation could be error and how to avoid it?</span></div>
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    <br>
    One could write a book in partial answer to this question. There are
    lots of things we don't yet know because we can't afford to run
    calculations that might yield knowledge. Ultimately, a model of
    physics is about as good as its capacity to reproduce findings from
    real physics, and so the goal of simulators should be to use methods
    that have been shown to do that well. Showing good performance can
    be tricky, as converged equilibrium distributions are normally very
    expensive to obtain. Also, different observables might require
    different methods for good agreement with experiment, so there is no
    general answer for how to do things right, unfortunately.<br>
    <br>
    Mark<br>
    <br>
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        <div><span></span>&nbsp;</div>
        <div><span>Cheers,</span></div>
        <div><span></span>&nbsp;</div>
        <div><span>Acoot</span></div>
        <div><br>
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        &nbsp;
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            <div dir="ltr"> <font face="Arial" size="2"> <b><span
                    style="font-weight: bold;">From:</span></b> Mark
                Abraham <a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au">&lt;Mark.Abraham@anu.edu.au&gt;</a><br>
                <b><span style="font-weight: bold;">To:</span></b>
                Discussion list for GROMACS users
                <a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org">&lt;gmx-users@gromacs.org&gt;</a> <br>
                <b><span style="font-weight: bold;">Sent:</span></b>
                Sunday, 1 April 2012 5:47 PM<br>
                <b><span style="font-weight: bold;">Subject:</span></b>
                Re: [gmx-users] Possible error in the gromacs
                calculation<br>
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              <div> On 1/04/2012 5:44 PM, Acoot Brett wrote:
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                    <div><span>Dear All,</span></div>
                    <div><span></span>&nbsp;</div>
                    <div><span>For the GROMACS 4.5.5, after installation
                        the test link is unavaliable, thus we cannot run
                        the test.</span></div>
                    <div><span></span>&nbsp;</div>
                    <div><span>For the AMBER, after we install it and
                        run the test, although we can pass most of the
                        tests, we cannot pass all of the tests.</span></div>
                    <div><span></span>&nbsp;</div>
                    <div><span>For GROMACS, can there anything wrong for
                        the calculation, just as if we cannot pass all
                        the test for AMBER?</span></div>
                    <div><span></span>&nbsp;</div>
                    <div><span>For the caluclation itself, in which
                        situation we can get the wrong calculation
                        results? And how should we solve the problems if
                        we the calculation can give wrong results by
                        default?</span></div>
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                <br>
                Unfortunately there is not an effective test set for
                GROMACS at the moment. There is work taking place to get
                one, but it will not be ready before 4.6.<br>
                <br>
                Mark<br>
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