[gmx-users] Problems with large molecule simulation

[Ben Tam]

Dear gromacs user,

I am trying to simulate a large system, but I ran into some fundamental problems. For example in the .gro file, the name of the atoms merge with the number count:

    2MOL     C2 9998   3.987   2.259   6.276
    2MOL     C5 9999   3.987   2.061   6.079
    2MOL     C110000   3.987   1.025   7.721
    2MOL     C210001   3.987   0.920   7.615

Sorry for this basic question, but how do people solve that problem? As I know there is a specific format for .gro file?

Thank you very much for your help.

Best regards,

Benjamin Tam