No curve obtained when opening potential.xvg with xmgrace

User discussions
1

GROMACS version: 2024
GROMACS modification: Yes/No
Here post your question

gmx energy -f em.edr -o potential.xvg

type “10 0” to select Potential (10); zero (0) terminates input.

xmgrace potential.xvg

Result: no curve is visable. The potential.xvg has been uploaded.

potential.xvg (25.0 KB)

2

The problem is the scale of the plot. Check the range of the y axis. The values drop so quickly it’s difficult to see anything:

    0.000000  1256710016.000000
    1.000000  37670224.000000
    2.000000  4075839.500000
    3.000000  324719.531250
    4.000000  -197021.078125
    5.000000  -304883.125000
    6.000000  -359751.250000
    7.000000  -444919.250000
    8.000000  -600577.250000
    9.000000  -695214.062500
   10.000000  -707332.062500
...

In xmgrace you can also address this by changing the max value of the y axis from 2e+09 to 2e+06.

3

OK. Moreover, does a sharp drop suggest there is something wrong in preparing molecular dynamics?

4

No, that’s good. You want the potential energy to go down during energy minimization. Perhaps there were some close contacts or unfavourable angles in the starting structure that gave a very high potential energy. As long as the energy minimization continues fine there’s no need to worry about the large drop.