On 16/03/11, "C.Y. Chang" <chiayun.ch...@gmail.com> wrote: > Hi, > > I try to calculate the Hbond in the ligand and remove the duplicate atoms in > the .ndx file dumped from g_hbond. > This is the contents in the .ndx file. > > [ HBD ] > 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 > > [ HBA ] > 17367 17375 17381 17384 17387 17388 17400 17404 17412 17418 17421 > 17424 17425 17437 17441 > 17449 17455 17458 17461 17462 17474 17478 17486 17492 17495 17498 > 17499 17511 17515 17523 > > 17529 17532 17535 17536 17548 > > And then, I perfrom the grompp. > It shows the error msg. > > Fatal error: > atoms 17366 and 17367 in charge group 1 of molecule type 'LIG' are in > different energy groups > > > How should I deal with the problem? >
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. > On the other side, I read the information in the web page > (http://www.mail-archive.com/gmx-users@gromacs.org/msg34617.html) > > I remove the lines in the [bonds] region in .top files. > But I still get these terms > > 1 Angle 2 G96Angle 3 Proper-Dih. 4 > Ryckaert-Bell. > 5 Improper-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) > > 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 > Position-Rest. > 13 Potential 14 Kinetic-En. 15 Total-Energy 16 Temperature > 17 Pres.-DC 18 Pressure 19 Constr.-rmsd 20 Box-X > > 21 Box-Y 22 Box-Z 23 Volume 24 Density > 25 pV 26 Enthalpy 27 Vir-XX 28 Vir-XY > 29 Vir-XZ 30 Vir-YX 31 Vir-YY 32 Vir-YZ > > 33 Vir-ZX 34 Vir-ZY 35 Vir-ZZ 36 Pres-XX > 37 Pres-XY 38 Pres-XZ 39 Pres-YX 40 Pres-YY > 41 Pres-YZ 42 Pres-ZX 43 Pres-ZY 44 Pres-ZZ > > 45 #Surf*SurfTen 46 Mu-X 47 Mu-Y 48 Mu-Z > 49 Coul-SR:LIG-LIG 50 LJ-SR:LIG-LIG > 51 Coul-14:LIG-LIG 52 LJ-14:LIG-LIG > 53 Coul-SR:LIG-DPPC_SOL 54 LJ-SR:LIG-DPPC_SOL > > 55 Coul-14:LIG-DPPC_SOL 56 LJ-14:LIG-DPPC_SOL > 57 Coul-SR:DPPC_SOL-DPPC_SOL 58 LJ-SR:DPPC_SOL-DPPC_SOL > 59 Coul-14:DPPC_SOL-DPPC_SOL 60 LJ-14:DPPC_SOL-DPPC_SOL > 61 T-DPPC 62 T-SOL 63 T-LIG 64 Lamb-DPPC > > 65 Lamb-SOL 66 Lamb-LIG > > And I try to remove lines in [bonds], [pairs], [angles] and [ dihedrals ], > but it is the same. > Where is the wrong process? And how could I get the angle and dihedral energy > in the intramolecules? > > Thanks for your any comments. > 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 :-) Mark > > Best, > > Chia-yun > > > 2011/3/14 Mark Abraham <mark.abra...@anu.edu.au> > > > > > > > > On 14/03/11, "C.Y. Chang" <chiayun.ch...@gmail.com> wrote: > > > > > > Hi, > > > > > > I try to calculate hydrogen bond (HB) energy. > > > The g_energy does not have this term. > > > And I find the g_hbond function in Gromacs. > > > But the HB energy calculation is not in g_hbond. > > > > > > > > > > > There's good reasons for this. How would you define the "HB energy" in > > terms of the kind of information accessible to MD simulations? > > > > > > > > > > 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 > > > > > > But there is a error msg, > > > > > > Atom 17380 in multiple Energy Mon. groups > > > > > > > > > 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. > > > > > > > > > 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. > > > > > > > > > I could set up the energy_grp and calculate energy between the ligand > > > group and the lipid layer group. > > > But I need the intramolecular energy in the groups. > > > How should I deal with these problems? > > > > > > > > > > > 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 > > > > > > Mark > > > > -- > > > > gmx-users mailing list gmx-users@gromacs.org > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > > Please don't post (un)subscribe requests to the list. Use the > > > > www interface or send it to gmx-users-requ...@gromacs.org. > > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > >
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