Dear manjula kasinathan
There aren't the "warning" parameter in gromacs, please remove the warning option in your mdp, if you need, add the flag -maxwarn in the grompp command, grompp -f pr.mdp -c em.gro -p top.top -o pr.tpr -maxwarn 10 your simulation presents Lincs warnings, read the gromacs's errors page: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings good luck Jessé
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