Need a help regarding NBFIX function

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

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.

Hi Prof. Lemkul,

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

HT 1 1.008000 0.417 A 0.0400013524445 0.192464

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


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.