[gmx-users] Re: Creating an atomtype where all nonbonded interactions are enumerated

[Andrew DeYoung]

Justin,

Thank you so much for your help!  That was really helpful.

It seems that I simply append my [ nonbond_params ] section to the end of my
ffnonbonded.itp file.  However, if I ONLY have this:

---
; ffnonbonded.itp
[ atomtypes ]
;type at.n	mass	charge  ptype  sig  eps
; all of the liquid atomtypes
; ...

[ nonbond_params ]
; i j func sig eps
mywall N 1 0.29750 4.56912
mywall C 1 0.31200 3.07524
mywall H 1 0.26170 1.17675
mywall B 1 0.31225 3.48667
mywall F 1 0.28974 2.82420
---

then I get an error message saying that atomtype mywall does not exist.
However, if I simply add a bogus entry for mywall in the [ atomtypes ]
section of ffnonbonded.itp, then grompp runs fine:

---
; ffnonbonded.itp
[ atomtypes ]
;type at.n	mass	charge  ptype  sig  eps
mywall 6  12.01100  0.000 A 0.00000e-1 0.00000e-1 ; bogus sig and eps
; all of the liquid atomtypes
; ...

[ nonbond_params ]
; i j func sig eps
mywall N 1 0.29750 4.56912
mywall C 1 0.31200 3.07524
mywall H 1 0.26170 1.17675
mywall B 1 0.31225 3.48667
mywall F 1 0.28974 2.82420
---

Is there any way that I can verify that the code is actually using the
parameters for mywall in the [ nonbond_params ] section, rather than the
bogus parameters (0 for sig and eps) for mywall in the [ atomtypes ]
section?

Thank you kindly!

Andrew DeYoung
Carnegie Mellon University