gmxcheck_d: 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_d - from package: gromacs

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

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