I wanted to ask how can we isolate the "protein.pdb" file during MDS run in different time intervals (such as 100ps, 500ps, 1000ps, 5000ps etc...)
One can monitor the progress of the simulation during the run, but it is very unwise to be operating on the trajectory that is being actively written. You could easily corrupt the file. You could, of course, copy it to another name and then work with it that way, but that might take up a lot of disk space.
You can use following command in gromacs:
trjconv -f md.xtc -s md.tpr -o output100ps.pdb -dump 100
(-dump 100 means coordinates at 100 picoseconds)
similarly you can use -dump 500 for 500 picoseconds.
That Sandeep Singh said, is completely true and the easiest way, I guess. The other option is charge the trajectory file into a visualization program like VMD and select the snapshot that you want, saving the coordinates. Furthermore, some MD software allow you to save a PDB file every x steps, so depending on which you are using, so this is another option.
Hello Sandeep Sir,
Can you please specify me, when this command has to be used at what stage??? During analysis or during molecular dynamic run???
I could answer. Has to be use once the simulation is finished, i.e.m, during the analysis of the results.
Take a look to the gromacs online manual, everything regarding commands and its performance is explained.
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