[gmx-users] Energy calculation

Wed Mar 16 09:22:20 CET 2011

On 16/03/11, "C.Y. Chang"  <chiayun.chang at 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.abraham at anu.edu.au>
> 
> 
> > 
> > 
> > On 14/03/11, "C.Y. Chang"  <chiayun.chang at 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
> > 
> > --
> > 
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> 
> 
> 
> 
> 
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