[gmx-users] How to efficiently fix pbc trajectories problems for VMD using

Vito Genna Vito.Genna at iit.it
Mon May 19 15:36:00 CEST 2014

Hi to everybody,

My name is Vito and I would like to share with you (and discuss also) the problems that I have found during my TRJs analysis.
I have a system made by: Protein + dsDNA + Ligand. I obtained my single precision trajectory in a .xtc file.
Well, I'd like to analyze my TRJs using VMD due to its intrinsic velocity in calcuating (Distances, angles, RMSD and so on) but I cannot do it because I encounter a serious issue with the visualization (pbc problems as you surely know)
To try to avoid the problem I've used several protocols, without success:


a) trjconv_mpi -f md_0_1.part0001.xtc -o md_0_1-whole.xtc -s md_0_1.tpr -pbc whole (on the entire system)
b) trjconv_mpi -f md_0_1-whole.xtc -o md_0_1-nojump.xtc -s md_0_1.tpr -pbc nojump
(on the entire system)
c) trjconv_mpi -f md_0_1-nojump.xtc -o md_0_1-fit.xtc -s md_0_1.tpr -fit progressive (on Protein only)

It does not work.


a) trjconv_mpi -f (as the previous one) -pbc mol -ur compact -center -o compact.xtc

It does not work as well.

3) Option 2 changing the flag -pbc mol with -pbc res

It does not work.

New idea? New possible combo?

Thanks in advance for your replies.

All the best


Vito Genna, PhD-Fellow
Italian Institute of Technology
Drug Discovery and Development department
Via Morego 30, 16163 Genoa, Italy

The process of scientific discovery is, in effect, a continual flight from wonder.
Albert Einstein

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