Pressure off due missing LJ parameters

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

1 Like

I think you didn’t quote the message correctly. I think it said: “The average pressure is off by at most 0.23 bar due to missing LJ interactions”. It is not your parameters that are the problem. See Too high pressure due to missing dispersion interactions in systems with no or weak electrostatics (#4861) · Issues · GROMACS / GROMACS · GitLab for more information.

Hello Magnus,

Thank you for your reply.

Yes you are right, I did not copy the exact message line and missed the part saying “average pressure”. I did not know if it was crucial.

The link was really helpful and now I can set up my simulation correctly based on the suggestions in the post.

Thanks, and regards,
Chaitanya

Regarding the quote, it was more the “… missing LJ parameters” part I meant was wrong, and I thought that was perhaps confusing you.

Hi Magnus,

I see. Thank you for patiently pointing it out.

Regards,
Chaitanya