[gmx-users] mdrun outputs incorrect resnames
mark.j.abraham at gmail.com
Sun May 26 00:57:21 CEST 2013
AFAIK, the residue names in the mdrun output .gro file are those of the
structure file you gave to grompp.
On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn <rvanlehn at gmail.com> wrote:
> I am simulating a lipid bilayer and wish to apply position restraints to
> only a subset of the lipids in the bilayer. Since position restraints are
> applied to all molecules of the same molecule type, I defined a new
> molecule type (DOPR) which is identical to my lipid species (DOPC) by
> copying the lipid itp file, renaming it and renaming the corresponding
> molecule type. I then manually edited a starting .gro file to change a
> subset of the DOPC molecules to DOPR, edited my topology,
> renumbered/reordered, etc. I also recreated the index file to account for
> the new molecules so that temperature coupling could be used correctly.
> Everything seemed ok when I ran the mdrun - grompp didn't complain, the
> program ran normally, the output trajectory clearly used the correct
> position restraints, etc. The weird part, though, is that the output .gro
> file at the end of the simulation only had DOPC molecules in it - the DOPR
> molecules that I had renamed by hand had somehow been output as DOPC
> instead. Positions, number of atoms, everything else was fine, just the
> name of the residues was different. I can't figure out why this is
> happening. It was reproducible across both GMX 4.5.5 / 4.6 and multiple
> different starting files.
> It's not a huge issue since the trajectories themselves are fine, I'm just
> worried this issue might indicate other, less obvious problems. A snippet
> of the topol file is below if that is helpful.
> Any suggestions / advice would be appreciated!
> #include "forcefield.itp
> #include "dopc.itp"
> #ifdef POSRES
> #include "dopc-posre.itp"
> ; Always include DOPR restraints for restrained lipids
> #include "dopc_restrained.itp"
> #include "dopr-posre.itp"
> #include "spc.itp"
> #include "ions.itp"
> [ system ]
> ; Name
> frame t= 1.000 in water
> [ molecules ]
> ; Compound #mols
> DOPC 398
> DOPR 2
> SOL 63882
> NA 179
> CL 179
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