Simulation of two organic molecules

User discussions
1

GROMACS version: 2020
GROMACS modification: No

I am trying to perform MD of two organic molecules. I have generated .itp; .prm; top files for both. Can anyone please guide me how to proceed further? I am not able to compile the topology file.

2

The topology is rather simple, e.g.

#include "parent.ff/forcefield.itp"
#include "any_new_parameters.itp"
#include "lig1.itp"
#include "lig2.itp"
#include "water.itp"

[system]
molecules in water

[molecules]
LIG1 1
LIG2 1
SOL X
3

Thanks for your reply.

But What about .prm ?

My single molecule topology is as mentioned below,

#include “charmm36-jul2021.ff/forcefield.itp”

; additional params for the molecule
#include “unl1.prm”

#include “unl1.itp”

#include “charmm36-jul2021.ff/tip3p.itp”
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “charmm36-jul2021.ff/ions.itp”

[ system ]
; Name
mol

[ molecules ]
; Compound #mols
UNL1 1

4

Those are new parameters. My example above just calls this “any_new_parameters.itp”

There may be other things you wish to add, like restraints, etc. but what I showed is a minimal example of how you can get things working.