[gmx-users] mdrun outputs incorrect resnames

Reid Van Lehn rvanlehn at gmail.com
Sun May 26 00:31:41 CEST 2013


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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