<br /><br /><span>On 14/03/11, <b class="name">"C.Y. Chang" </b> <chiayun.chang@gmail.com> wrote:</span><blockquote cite="mid:AANLkTiktS1hZmjv3iziC2iG84M1DkgzB_98=6JyDBzoX@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Hi,<br /><br />I try to calculate hydrogen bond (HB) energy.<br />The g_energy does not have this term.<br />And I find the g_hbond function in Gromacs.<br />But the HB energy calculation is not in g_hbond.</div></blockquote><br />There's good reasons for this. How would you define the "HB energy" in terms of the kind of information accessible to MD simulations?<br /><br /><blockquote cite="mid:AANLkTiktS1hZmjv3iziC2iG84M1DkgzB_98=6JyDBzoX@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Therfore, I also try to dump the .ndx file including the HB_donor, HB_acceptor and HB_system from g_hbond, and perfrom the grompp<br />
But there is a error msg,<br /><br />Atom 17380 in multiple Energy Mon. groups</div></blockquote><br />Look up energy groups in the manual - start of section 3.3. Your .mdp file is defining an illegal combination of atoms and energy monitor groups.<br /><br /><blockquote cite="mid:AANLkTiktS1hZmjv3iziC2iG84M1DkgzB_98=6JyDBzoX@mail.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html">Another problem is about calculating the intramolecular energy e.g. 1,4-nonbonded, van der waal, electrostatic etc. of the ligand in lipid layer-ligand complex system.<br />
I could set up the energy_grp and calculate energy between the ligand group and the lipid layer group.<br />But I need the intramolecular energy in the groups.<br />How should I deal with these problems?</div></blockquote><br />An inter-group energy doesn't mean anything much, so don't bother. Please read the whole of this thread http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html<br /><br />Mark