[gmx-users] Question

Justin Lemkul jalemkul at vt.edu
Thu Oct 23 22:39:59 CEST 2014

On 10/23/14 4:29 PM, Eric Smoll wrote:
> Hello Gromacs users,
> If I have all the files that were used to generate a trajectory file, what
> is the proper procedure to update the atomnames in the trajectory. My best
> guess is below. Is this problematic?
> # remove first frame of trajectory
> cat << EOF > tmp.ndx
> 1
> trjconv -fr tmp.ndx -f old.trr -s old.tpr -o tmp.gro
> # Edit tmp.gro and rename edit.gro
> # Edit old.itp to edit.itp
> # Edit old.top tp edit.top
> grompp -f old.mdp -c edit.gro -p edit.top -o edit.tpr
> trjconv -s edit.tpr -f old.trr -o new.trr

Why do you need new atom names?  Since atom names are not stored in the 
trajectory, it is simple to change the input to have things reinterpreted:

1. Edit topology that contains atom names to be changed.
2. Run grompp with original coordinate file, new topology, and -maxwarn 1 
(because it will complain about mismatching atom names, but will override those 
in the coordinate file with whatever is in the topology)
3. Carry out whatever analysis you wanted with the new atom names
4. Profit?



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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