[gmx-users] crystals of KCl during simulation

Rebeca García Fandiño regafan at hotmail.com
Mon Jun 1 13:24:44 CEST 2009

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?

Thank you very much in advance for your help.

Rebeca Garcia 
Academic Visitor
Dep. of Biochemistry
University of Oxford

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