Creating nacl in water system

User discussions
,
1

GROMACS version: 2018.6
GROMACS modification: No

I am very new to using gromacs, so I would appreciate any input.
I am trying to set up a system of NaCl (JC) in water(spce) . I was able to run the tutorial simulation of lysozome in water. But in this the topology file was created rather easily using pdb2gmx. I dont know how to create a topology file for water in nacl system.

I tried generating a box of water using

gmx solvate -box 11 -cs spc216.gro

But am not able to proceed with replacing water with ions using genions because when i try to use grompp it shows fatal error.

This is the topology file i used
IMG_20220530_151817_484

And this is the error I am getting

Program: gmx grompp, version 2018.6
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 799)

Fatal error:
Syntax error - File spc.itp, line 1
Last line read:
‘[ moleculetype ]’
Invalid order for directive moleculetype

2

You need to introduce a parent force field first, or at least a [defaults] directive and any associated parameters for any species in your system, before you can define any actual molecules.

A generic topology structure is as simple as:

#include "parent.ff/forcefield.itp"
#include "water_model.itp"
#include "ions.itp"

[system]
nacl in water

[molecules]
SOL X
NA  Y
CL  Z
3

Thanks lot for your guidance. It helped alot.