How do we use gmx polystat?

User discussions
1

Hi All,

My system contains 60 polymers and I want to calculate the average end-to-end distance change with time. In the index file if I define indexes of the starting end and the ending end of the polymer with the following command would it give me the average end-to-end distance with time?

gmx polystat -s …/…/…/run.tpr -f run0-14_nopbc.xtc -o 0.xvg -n index.ndx

My index file looks as follows. For each line, it contains indexes for the starting end and end atom index

[ poly60 ]
6 149
164 307
322 465
480 623
638 781
796 939
954 1097
1112 1255
1270 1413
1428 1571
1586 1729
1744 1887
1902 2045
2060 2203
2218 2361
2376 2519
2534 2677
2692 2835
2850 2993
3008 3151
3166 3309
3324 3467
3482 3625
3640 3783
3798 3941
3956 4099
4114 4257
4272 4415
4430 4573
4588 4731
4746 4889
4904 5047
5062 5205
5220 5363
5378 5521
5536 5679
5694 5837
5852 5995
…

2

That should work. Have you tried?

3

@hess Yes, I tried. However, I was unsure whether I needed to provide all indexes (all atoms) in the index file. That way too, I can get values and have doubts about which way is correct.

Thank you for clearing my doubts. So now I know that I need to provide only the indexes of the two ends to get the correct end-to-end distance of the polymer.