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?
Thank you very much in advance for your help.
Rebeca Garcia
Academic Visitor
Dep. of Biochemistry
University of Oxford
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