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Hello people,<br><br>My professor and I tried to use the FENE potentials to relax a protein from a unstable configuration for publishing paper. However, these potentials didn't seem to work. Checking both the manual and the code of the GROMACS software package for moleculair dynamics we found some things we do not understand both me as even my professor.<br><br>First one thing:<br><br> In file bondfree.c in gmxlib the force constant kb (parameter: real kb) for the FENE potential is not included anywhere in the force neither potential calculation . <br><br> bm = forceparams[type].fene.bm; <br> kb = forceparams[type].fene.kb;<br> bm2 = bm*bm;<br><br> omdr2obm2 = one - dr2/bm2;<br><br> vbond = -half*bm2*log(omdr2obm2);<br> fbond = -bm/omdr2obm2;<br><br><br>Second one next thing:<br><br>In the following lines:<br><br>The scalar force is composed over its dimension by dx[m]:<br><br>fij=bond*dx[m]<br><br>However in stead of taking a unit normalized vector the original connecting vector is taken. The manual isn't clear about this either, but looking at the equations it doens't make a lot of sense to me and my professor to use the original connecting vector.<br><br>Greetings from China,<br><br>Jiang<br><br><br><br><br><br><br><br /><hr />Live Earth is coming. Learn more about the hottest summer event - only on MSN. <a href='http://liveearth.msn.com?source=msntaglineliveearthwlm' target='_new'>Check it out!</a></body>
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