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

Dallas Warren dallas.warren at monash.edu
Tue Jul 18 03:33:43 CEST 2017

First thing you should do is try it out and find out for yourself.
Far faster and far more educational for yourself.

Did you try both of those options out?  What differences did you observe?

Read http://manual.gromacs.org/online/tpr.html to see why those
scripts require the tpr file.  What is/are the difference(s) between
the two tpr files you have available in those two options?  Is/are
that/those difference(s) going to make a difference to how the hbond
script performs and the results it obtains?

tl;dr it will make no difference

But don't take my word for it, because I could be wrong, and I'm just
some internet random, try it out and provide it to yourself.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 18 July 2017 at 04:38, Adarsh V. K. <adarsh_p130085bt at nitc.ac.in> wrote:
> 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
> --
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