[gmx-users] Position restraints with Martini force field

[ARNAB MUKHERJEE]

Hi everyone,

I am simulating a DNA protein system with Martini forcefield. I want to use
position restraints on all DNA atoms. So I used gmx genrestr command to
generate .itp file for position restraints of all the DNA atoms. So without
including position restraints, my .top file looks like this :
 #include "martini_v2.1-dna.itp"
#include "martini_v2.0_ions.itp"

#define RUBBER_BANDS

#include "Nucleic_A+Nucleic_B.itp"
#include "Protein_A.itp"

[ system ]
; name
Martini system from DNA-CG.gro

[ molecules ]
; name        number
Nucleic_A+Nucleic_B      1
Protein_A        1
W           207523
NA               238
CL               21

Here all the .itp files are from Martini force field. It works fine without
problem.

Now when I include the position restraints, my .top file looks like the
following :

#include "martini_v2.1-dna.itp"
#include "martini_v2.0_ions.itp"

#define RUBBER_BANDS

#include "Nucleic_A+Nucleic_B.itp"
#include "posre_DNA.itp"
#include "Protein_A.itp"

[ system ]
; name
Martini system from DNA-CG.gro

[ molecules ]
; name        number
Nucleic_A+Nucleic_B      1
Protein_A        1
W           207523
NA               238
CL               21

So the only difference is that I included here the position restraints .itp
file generated using gmx genrestr (posre_DNA.itp) just below the DNA .itp
file (Nucleic_A+Nucleic_B.itp).

My doubt is that is this the right way to use position restrains? Is the
location in the .top file where I included  posre_DNA.itp file, correct?

I would highly appreciate any help.

Thank you very much,

Regards,

Arnab