mdrun: 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/mdrun - from package: gromacs

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

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