[gmx-users] crystals of KCl during simulation

[Mark Abraham]

Rebeca García Fandiño wrote:
> Hi,
> I am trying to simulate a protein in aqueous solution 1M (KCl) with 
> Gromacs and using the amber force field.
> 
> I get the topology of the solvated protein - without the ions- from 
> amber (Leap) and then used the script amb2gmx.pl to obtain the Gromacs 
> .top and .gro files.
> I did not introduced the ions from Amber because amb2gmx.pl is only 
> written for NaCl, so I used genion to ionize the system.
> I added the lines correspondent to the ions in Amber to the .top of Gromacs:
> 
> [ atomtypes ]
> amber99_51     K      0.0000  0.0000  A   4.73602e-01  1.37235e-03 ; K+ ion
> amber99_30    Cl      0.0000  0.0000  A   4.40104e-01  4.18400e-01 ; Cl- ion
> 
> [ moleculetype ]
> ; molname       nrexcl
> K               1
> 
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>      1  amber99_51  1    K      K       1       1       39.10000
> 
> [ moleculetype ]
> ; molname       nrexcl
> Cl              1
> 
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr     charge       mass
>      1  amber99_30  1    Cl     Cl      1      -1       35.45000
> 
> and everything went OK, but after equilibration I have observed that KCl 
> is aggregating, like if it was making crystals. When I used NaCl instead 
> KCl, this not happened.
> 
> Does anybody has any idea about the reason of the behaviour of KCl in 
> the simulation?

You may have supplied LJ parameters that are not appropriate for the LJ 
  type and combination rule in force. Compare the magnitudes of the 
final two parameters with the other ffamber ion [ atomtype ] entries. 
Also see header section of ffamber.itp and relevant manual sections.

Mark