[gmx-users] Energy calculation

C.Y. Chang chiayun.chang at gmail.com
Wed Mar 16 09:03:03 CET 2011 

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?



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.
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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