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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
