[gmx-users] How to analyze after extending a simulation?

[Adarsh V. K.]

Dear all,


*1) I used following command to extend a completed simulation*
gmx convert-tpr -s md_0_1.tpr -extend 20000 -o tpxout.tpr

gmx mdrun -deffnm tpxout -cpi md_0_1.cpt -v


*2) Combined the trajectories using the command*
gmx trjcat -f *.xtc -o full.xtc

*3) Now what command to use for H bond analysis (A or B)*

A).
gmx trjconv -s md_0_1.tpr -f full.xtc -o full_noPBC.xtc -pbc mol -ur compact
gmx hbond -s md_0_1.tpr -f full_noPBC.xtc -num hbnum.xvg

B).
gmx trjconv -s tpxout.tpr -f full.xtc -o full_noPBC.xtc -pbc mol -ur compact
gmx hbond -s tpxout.tpr -f full_noPBC.xtc -num hbnum.xvg