Allen Smith wrote:
In message <[EMAIL PROTECTED]> (on
3 October 2007 19:13:51 +0200), [EMAIL PROTECTED] (maria goranovic)
wrote:
Hi,
I had a large bilayer in .gro and .top gromacs format files
Bilayer? I believe there are some specific things for doing planar periodic
boundary conditions (or planar infinite system conditions), but I am not
familiar with them.
Yeah but they're in the .mdp and not the issue here :-)
which I truncated to make a smaller bilayer, and added some more water
molecules, using programs other than gromacs. The final output I have is a
pdb file with complete solvation, and a topology file which I obtained from
the original top file by simply changing the number of residues of each
group in the last section.
Umm... the atom numbers (not just the numbers of residues) are going to need
to correspond between the .top and .gro files.
I think the OP meant changing the number of molecules in the [molecules]
section of the .top file. I expect that within each molecule in the
structure file the order of the atoms must agree between with the
topology file. Certainly the order of the molecules in the [molecules]
section must correspond to that in the structure file.
However, the atom numbers cannot (in general), match in order between
structure and topology file for any system with more than one copy of a
molecule (e.g. solvent). For simple solvated systems where one gets
focussed on the solute, it can look like correspondence is occurring and
thus might be necessary :-)
Mark
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