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.
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.
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
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
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.