Need a help regarding NBFIX function

User discussions
1

GROMACS version: GROMACS 2018
GROMACS modification: No

Dear GROMACS user,

I want to simulate an intrinsically disordered protein using Charmm36mW force field. Actually, I followed 2017 Nature Method paper.

According to this paper, I need to increase εH value from −0.046 to −0.1 kcal/mol. I saw a nbfix.itp in the charmm force-field folder. Do I need to add the change in the nbfix.itp file. I am bit confused regarding this issue.

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee

2

The C36 port does not support this water model. If you want to implement this modified water model, adjust the H ε in ffnonbonded.itp and then create two NBFIX entries in nbfix.itp to restore the normal CHARMM TIP3P H-H and H-O LJ interactions. The only interactions that should be modified are those between the protein and water. Water-water interactions need to remain unperturbed, which may not be obvious from the way the paper was written but is how it should be carried out.

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Hi Prof. Lemkul,

Thank you very much for your kind advice. I just need to adjust in ffnonbonded.itp in the following lines.

; CHARMM_TIP3P, but not HEAVY_H
HT 1 1.008000 0.417 A 0.0400013524445 0.192464

Or, I need to adjust in [ pairtypes ] also. Please let me know.

Regards,
Snehasis

4

You do not need to do anything with pairs, since those are 1-4 interactions and therefore are not relevant to water. You also need to add NBFIX terms. Adjusting the LJ of the HT type alone is not sufficient. See my post above.