<br><br><div><span class="gmail_quote">On 7/11/06, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org
</a></b> <<a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br> <a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
gmx-users@gromacs.org</a><br>From: "Berk Hess" <<a href="mailto:gmx3@hotmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx3@hotmail.com</a>><br>Subject: Re: [gmx-users] Energy profile with umbrella sampling
<br><br>>From: "pim lists" <
<a href="mailto:pimlists@googlemail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">pimlists@googlemail.com</a>><br>>>We are using umbrella sampling to observe a hydrogen transfer. And would
<br>>>like to analyze our results by graphing the energy against the reaction
<br>>>coordinates, in order to see the energy profile for the transition state.<br>>>Does the force constant from the umbrella sampling affect the output of<br>>>g_energy? Are there any special steps that should be taken in order to do
<br>>>this?<br>>><br>>>Thank you for your time and assistance<br>>><br>>>Robert Fiske<br>>><br>><br>>According to src/mdlib/pull.c the umbrella forces*displacement are added to<br>
>the virial. Therefore I'd say you see back effects in the virial/pressure<br>>output of g_energy.<br>>The umbrella potential energy is apparently not written away anywhere,<br>>you'll have to recalculate it from the displacement-from-the-mean written
<br>>in<br>>your pull.pdo output file, and add that energy yourself to the total<br>>energy.<br><br>Indeed it does not seem to be added to the total energy,<br>this should be stated in the manual.<br><br>But anyhow, in most cases you do not want this contribution to the energy,
<br>as you would like to have the energy of the original system.<br>The only thing that you need to correct for is that the sampling<br>is biased by the umbrella potential, which you can recalculate from<br>the displacement and the force constant.
<br><br>Berk.<br></blockquote></div><br>
Sorry, I must have been sleeping! In any case, you state you want an
energy profile for the transition state. Interaction energies you can
get correctly from the g_energy file, but I guess you want free
energies. How could you retrieve those? Boltzmann inversion of the
distance distribution of your coordinate + the correction of the
umbrella potential?<br>
<br>
greetings, Pim<br>
<br>