[gmx-users] trjconv - pbc centering and fitting

[Nixon Raj]

HI everyone,


I have crystal structure output from pdb2gmx *eg. aaa.gro*



After my 200ns production run , i ran trjconv as below

1. trjconv -n ../index.ndx -f md.xtc -s em.tpr -o md.pbc.xtc -ur rect
-boxcenter rect -pbc nojump

2. trjconv -n ../index.ndx -f md.pbc.xtc -s em.tpr -o md.center_mol.xtc
-center -ur rect -boxcenter rect -pbc mol

3. trjconv -n ../index.ndx -f md.center_mol.xtc -s em.tpr -o md.center.xtc
-center -ur rect  -boxcenter rect

4. trjconv -n ../index.ndx -f md.center.xtc -s em.tpr -o md.fitprog.xtc -fit
progressive

5. trjconv -n ../index.ndx -f md.fitprog.xtc -s em.tpr -o *md.fit.xtc* -fit
rotxy+transxy


And finally i have md.fit.xtc which is reduce to 1000 frames using -dt 200

*Note: em.tpr is the tpr file for minimization (crystal structure after
solvation and genion )*

Now, when i load in VMD

1. my crystal structure - *aaa.gro *as reference

2.my production *frame 0(md.fit.gro) with md.fit.xtc*

They were not fit over eachother instead they were apart.


*Am I wrong in my trjconv or my selection of reference structure???? PLease
help me*