----- Original Message ----- From: Moeed <lecie...@googlemail.com> Date: Friday, August 27, 2010 2:21 Subject: [gmx-users] making index file To: gmx-users@gromacs.org
> 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. That all sounds quite sensible, assuming your solvent is not water. > 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? The default index groups rely on the residue names being looked up in a database of residue types (IIRC in share/top/aminoacids.dat). You'd have to tweak that for it to work in your case. > > > 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?! That's the one you created. You merged residues 1, 2 and 3 into one group. However you want to merge whole groups, so you want "1 | 2 | 3". > > Residues a, b and c belong to solute and should form one group since I want > to get interaction energy Maybe residues are equivalent to molecules in your case, but I suspect the above comment indicates at least some confusion somewhere. A group can have many molecules which can have many residues. Or one molecule with one residue. Or some random set of atoms. You choose :-) > 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. make_ndx has a tiny help facility which is a useful reminder of how to do some things. Even using it to write out the [ System ] group to an index file, and then manually making a [ Solute ] group from that in a text editor is really not hard (hint: it should probably have the numbers 1 to 350 and nothing else) Mark
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