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
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