<br /><br /><span>On 16/03/11, <b class="name">"C.Y. Chang" </b> <chiayun.chang@gmail.com> wrote:</span><blockquote cite="mid:AANLkTiktngPZDM-qLXhL7=BgEMuOkskD0ZC53m65nhYg@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 the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond.<br />This is the contents in the .ndx file.<br /><br />[ HBD ]<br /> 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530<br />
[ HBA ]<br /> 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 17424 17425 17437 17441<br /> 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 17499 17511 17515 17523<br />
17529 17532 17535 17536 17548<br /><br />And then, I perfrom the grompp.<br />It shows the error msg.<br /><br />Fatal error:<br />atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in different energy groups<br />
<br />How should I deal with the problem?</div></blockquote><br />Redefine charge or energy groups as appropriate for whatever you're trying to do. Non-bonded interactions are calculated by looping over atom-atom interactions grouped by charge group and then by energy group. Every charge group must be a subset of an energy group or fully disjoint from it.<br /><br /><blockquote cite="mid:AANLkTiktngPZDM-qLXhL7=BgEMuOkskD0ZC53m65nhYg@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">On the other side, I read the information in the web page (<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html" target="1">http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html</a>)<br />
I remove the lines in the [bonds] region in .top files.<br />But I still get these terms<br /><br /> 1 Angle 2 G96Angle 3 Proper-Dih. 4 Ryckaert-Bell.<br /> 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR)<br />
9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Position-Rest.<br /> 13 Potential 14 Kinetic-En. 15 Total-Energy 16 Temperature<br /> 17 Pres.-DC 18 Pressure 19 Constr.-rmsd 20 Box-X<br />
21 Box-Y 22 Box-Z 23 Volume 24 Density<br /> 25 pV 26 Enthalpy 27 Vir-XX 28 Vir-XY<br /> 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ<br />
33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX<br /> 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY<br /> 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ<br />
45 #Surf*SurfTen 46 Mu-X 47 Mu-Y 48 Mu-Z<br /> 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG<br /> 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG<br /> 53 Coul-SR:LIG-DPPC_SOL 54 LJ-SR:LIG-DPPC_SOL<br />
55 Coul-14:LIG-DPPC_SOL 56 LJ-14:LIG-DPPC_SOL<br /> 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL<br /> 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL<br /> 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC<br />
65 Lamb-SOL 66 Lamb-LIG<br /><br />And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], but it is the same.<br />Where is the wrong process? And how could I get the angle and dihedral energy in the intramolecules?<br />
Thanks for your any comments.</div></blockquote><br />You're decomposing PME electrostatics. That produces garbage values for quantities that have little meaning, like it says in the thread I suggested you read the whole of. I'm going to stop helping :-)<br /><br />Mark<br /><br /><blockquote cite="mid:AANLkTiktngPZDM-qLXhL7=BgEMuOkskD0ZC53m65nhYg@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"><br />Best,<br /><br /> Chia-yun<br /><br /><br /><div class="gmail_quote">2011/3/14 Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span><br />
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br /><br /><span>On 14/03/11, <b>"C.Y. Chang" </b> <<a href="mailto:chiayun.chang@gmail.com" target="1">chiayun.chang@gmail.com</a>> wrote:</span><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>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 />
</div>There's good reasons for this. How would you define the "HB energy" in terms of the kind of information accessible to MD simulations?<div class="im"><br /><br /><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite">
<div>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 /></div>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.<div class="im">
<br /><br /><blockquote style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div>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 />
</div>An inter-group energy doesn't mean anything much, so don't bother. Please read the whole of this thread <a href="http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html" target="1">http://lists.gromacs.org/pipermail/gmx-users/2010-November/055687.html</a><br />
<font color="#888888"><br />Mark
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