Running GROMOS54A7 with TIP4P water

User discussions
1

GROMACS version: 2020.5
GROMACS modification: Yes

Hello,

I am trying to run a simulation of the thermoresponsive hydrogel Poly(N-isopropylacrylamide), as per the paper DOI: 10.1016/j.fluid.2010.03.025

In the paper, on page 20, they mention that they used GROMOS with TIP4P water to run their simulation. I have been trying to run this simulation, but I am facing quite a few hurdles. I know that TIP4P is not recommended with GROMOS, but I want to figure out how to run it, as a learning exercise.

Initially, I was getting the error, atomtype OWT4 not found, so I added it to atomtypes, and Tten, I added the TIP4P atomtypes in the GROMOS54A7_atb.ff/ffnonbonded.itp for tip4p water from CHARMM27.ff/ffnonbonded.itp.

I obtained the .itp and .pdb file for my polymer from ATB.
However, once I did that, I started getting the following error:
ERROR 1 [file topol.top, line 20]:
atom H29 (Res XCN0-1) has mass 0 (state A) / 0 (state B)

And I have 572 (!) of such errors, where
atom XXX (Res XCN0-1) has mass 0 (state A) / 0 (state B)

Is there a way to fix this error? How did the people who wrote that paper manage to pull this off?

I appreciate any advice you have for me.

2

You will need to transform the values from σ/ε to C6/C12 since these force fields use different conventions for the LJ expression.

Does execution of grompp work with unmodified force field files? The problem seems unrelated to water.

Write to the corresponding author and ask :)