gmxcheck: command not found

Maybe Your $PATH variable doesn't contain the default paths? echo $PATH should give something like:

[root@server ~]# echo $PATH
/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin

If it's empty, You may set the PATH variable with this command

export PATH="/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin"

On Debian possible default full paths are:

/usr/bin/gmxcheck - from package: gromacs

You may install the required package with command apt-get install {package}

Error in other languages:
gmxcheck: bevel nie gevind nie
gmxcheck: comandă negăsită
gmxcheck: comando não encontrado
gmxcheck: commande introuvable
gmxcheck: command not found
gmxcheck: käsku ei ole
gmxcheck: không tìm thấy lệnh
gmxcheck: komanda nerasta
gmxcheck: Kommando nicht gefunden.
gmxcheck: kommandot finns inte
gmxcheck: komut yok
gmxcheck: nie znaleziono polecenia
gmxcheck: níor aimsíodh an t-ordú
gmxcheck: no se encontró la orden
gmxcheck: no s'ha trobat l'ordre
gmxcheck: opdracht niet gevonden
gmxcheck: parancs nem található
gmxcheck: perintah tidak ditemukan
gmxcheck: príkaz nenájdený
gmxcheck: příkaz nenalezen
gmxcheck: команда не найдена
gmxcheck: командата не е открита
gmxcheck: 命令找不到
gmxcheck: コマンドが見つかりません