Hello Justin, Please let me explain my naive procedure to make index file so that you can make comment. I have created the top file for a single solvent molecule. Then removed [system] , [molecule] directives as well as "#ffgmx.itp". The [molecule type] is named 'solvent''. I got a sample itp file from a tutorial and then copied the contents of this modified top file into the file with itp extention and named it solvent.itp. Then I # included this itp file in solute. top file and based on solvated gro file added "solvent 1000" in [molecule] directive of solute.top. solvated gro contains residues a,b,c for solute and 'SOL' for the solvent. then I issue the command : make_ndx -f solvated.gro -o solvated.ndx which lists the residues :
0 System : 30350 atoms 1 a : 10 atoms 2 b : 330 atoms 3 c : 10 atoms 4 SOL : 30000 atoms I am not getting my default groups according to [moleculetype]. Am I missing sth? That I am only getting system index group is becase I am only using user defined residues? > r1|r2|r3 Merged two groups with OR: Merged two groups with OR: 5 r_1_r_2_r_3 : is giving me different directives for system, a, b, c, and SOL and one for r_1_r_2_r_3 in solvated.ndx. I dont see what the last one is for?! Residues a, b and c belong to solute and should form one group since I want to get interaction energy between solute and solvent. How can I create these two groups (to be included in mdp file energy groups ). I searched the manual and archive list but never found such details of creating index files. It seems it is something that everyone knows! :) Please help me.. thanks.
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