GROMACS version: 2024.1
GROMACS modification: Yes/No
Hello everyone,
I am not well versed with gromacs so wanted to clarify a few things and try to solve my problem. I am running a simulation with NaCl + K + F + Ar in water (spce) system. All the potentials are LJ potentials and I am using combination rule 2.
However, since I want to tweak some parameters for NaCl interaction, I specify the Na-Ar and Na-Cl parameters in the nonbond_params section.
In my understanding I have supplied all the non-bonded parameters, but in the log file I find the following line -
“Pressure off my at most 0.23 bar due to missing LJ parameters.”
This has got me worried as to which parameters I am missing and how to specify them.
Can anyone please guide me and clarify what the statement means and what mistake I may be making?
For reference, my topology file looks as follows:
! created by fftool; mix = g
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.5
[ atomtypes ]
; name at.nr mass charge ptype sigma epsilon
Na 11 22.9900 0.0000 A 2.15950e-01 1.47546e+00
Cl 17 35.4230 0.0000 A 4.83050e-01 5.34920e-02
K 11 22.9900 1.0000 A 2.15950e-01 1.47546e+00
F 17 35.4230 -1.0000 A 4.83050e-01 5.34920e-02
O 8 15.9990 -0.8476 A 3.16600e-01 6.50000e-01
H 1 1.0080 0.4238 A 0.00000e+00 0.00000e+00
Ar 11 22.9900 0.0000 A 16.0000e-01 0.00050e+00
[ nonbond_params ]
i j func sigma epsilon
Na Ar 1 0.90800e-01 0.00000e+00
Cl Ar 1 1.04200e-01 0.00000e+00
[ moleculetype ]
; name nrexcl
NaCl 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 Na 1 Na Na 1 0.000000
2 Cl 1 Cl Cl 1 0.000000
[ bonds ]
; ai aj func b0 kb
[ constraints ]
; ai aj func b0
[ pairs ]
; ai aj func
[ angles ]
; ai aj ak func th0 cth
[ dihedrals ]
; ai aj ak al func coefficients
#ifdef POSRES
#include "constr.itp"
#endif
[ moleculetype ]
; name nrexcl
K 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 K 1 K K 1 1.000000
[ bonds ]
; ai aj func b0 kb
[ constraints ]
; ai aj func b0
[ pairs ]
; ai aj func
[ angles ]
; ai aj ak func th0 cth
[ dihedrals ]
; ai aj ak al func coefficients
[ moleculetype ]
; name nrexcl
F 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 F 1 F F 1 -1.000000
[ bonds ]
; ai aj func b0 kb
[ constraints ]
; ai aj func b0
[ pairs ]
; ai aj func
[ angles ]
; ai aj ak func th0 cth
[ dihedrals ]
; ai aj ak al func coefficients
[ moleculetype ]
; name nrexcl
SPCE 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 O 1 SPC O 1 -0.847600
2 H 1 SPC H1 2 0.423800
3 H 1 SPC H2 3 0.423800
#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330
[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000
[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#endif
[ moleculetype ]
; name nrexcl
Ar 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 Ar 1 Ar Ar 1 0.000000
[ bonds ]
; ai aj func b0 kb
[ constraints ]
; ai aj func b0
[ pairs ]
; ai aj func
[ angles ]
; ai aj ak func th0 cth
[ dihedrals ]
; ai aj ak al func coefficients
[ system ]
simbox
[ molecules ]
NaCl 33
K 360
F 360
SPCE 2000
Ar 1
Thanks, and regards,
Chaitanya