#2 Generally a good idea to keep the names consistent, however - why are you using POP in the coordinate file instead of POPC? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Shima Arasteh <shima_arasteh2...@yahoo.com> wrote: Dear gmx users, I want to simulate POPC in water. In equilibration step, I have to make an index file. But when I enter this command, I do not know to choose which group to make a suitable .ndx file which matches the molecule types and molecules sections in .top file . The .top file contains these: [ moleculetype ] ; Name nrexcl POPC 3 . . . . [ system ] ; name POPC in water [ molecules ] ; name number POPC 128 SOL 3800 It is the command I enter: # make_ndx -f em.gro -o index.ndx 0 System : 18056 atoms 1 Other : 6656 atoms 2 POP : 6656 atoms 3 Water : 11400 atoms 4 SOL : 11400 atoms 5 non-Water : 6656 atoms nr : group ! 'name' nr name 'splitch' nr Enter: list groups 'a': atom & 'del' nr 'splitres' nr 'l': list residues 't': atom type | 'keep' nr 'splitat' nr 'h': help 'r': residue 'res' nr 'chain' char "name": group 'case': case sensitive 'q': save and quit 'ri': residue index Now, what is the correct answer? Anybody can suggest me? Thanks in advance, Shima ge
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