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<span>On 03/10/11, <b class="name">Sajad Ahrari </b>
<a class="moz-txt-link-rfc2396E" href="mailto:sajadahrari@yahoo.com"><sajadahrari@yahoo.com></a> wrote:</span>
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<div>Hello Dear users</div>
<div>is there any command in gromacs for analysis
of protein stability? or I should be using those
related to calculation of B-factor?</div>
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<br>
That's an extremely complex thing to attempt to measure. The
observables in MD simulations are the positions and velocities of
atoms. It is infeasible to simulate for long enough to measure
something like the free energy of folding. You might be able to
measure a relative stability using alchemical free energy methods,
but that's not exactly a beginner topic.<br>
<br>
Mark<br>
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