[gmx-users] SR and LJ energies

[Michal Kolinski]

Hi all.

 

I'm simulating receptor in membrane with ligand (morphine) inside the active site of the protein.  Topology for ligand I obtained using PRODRG  server (I checked it, and the topology seems OK).  My question is about LJ and Coulomb (ligand-receptor interaction) energies I got for my 1ns MD.  I wonder why all coulomb energies are so low?  Is it normal in gromacs? 

Can it be because of badly assigned charges to ligand by PRODRG?   (charge of ligand +1)

(system is well equilibrated, energies are stable, I'm using PME).

Please give me some comment on this.

Thank you in advance Michal.

 

Coul-SR:RECEP-MORP    LJ:RECEP-MORP

      -6,29808
     -271,43
     
      -4,92685
     -251,745
     
      -4,82635
     -278,962
     
      -5,66835
     -281,826
     
      -3,40901
     -274,985
     
      -7,47754
     -266,313
     
      -4,65743
     -291,132
     
      -3,87318
     -292,169
     
      -3,72551
     -279,625
     
      -4,10787
     -272,555
     
      -3,9129
     -281,472
     
      -5,66577
     -282,904
     
      -2,76462
     -263,837
     
      -3,92319
     -256,529
     
      -5,41663
     -276,039
     
      -4,9061
     -268,61
     

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