Hi, 

As far as I know this could happen for few reasons. Time step too high ( but I am guessing you are using standard 2fs), may be there are still bad contacts so you might need another energy minimization or try lesser value of emtol.  One other thing I know is, if you mention molecules in in a different place in *.top file compared to *.gro/*.pdb or vice-versa and you get a warning that there is mismatch of atoms between input files but you ignore it using maxwarn. 

Mr. Dhar,

Which program packages you have used? 

@Bojidarka  : Ma'am i am using gromacs (v 4.5.6) with gromos 54a ff.

@Vikas : Sir yes, time step is 2fs. Energy minimization step was proper, i guess (attaching final values). I did't get any warning during EM step as well as equilibrium step

Steepest Descents converged to Fmax < 1000 in 7857 steps

Potential Energy = -7.1789690e+06

Maximum force = 9.9025854e+02 on atom 5123

Norm of force = 6.5917387e+00

the initial input which i am using is a complex of 3 proteins, which goes well in simulation with water (normal) and completes the Em, Eq and MD run steps with proper  output. What i am trying is adding 10 to 20 molecules of ethylene along with water to check the changes in trajectory. More precisely, i want ethylene in close proximity of my protein complex. First i tried to define the box dimensions, then tried to insert molecules in center. Unfortunately none of above worked for me. So , i thought that some how packaging of system is not proper, thus getting this error.

Any suggestions for system building procedure ?@Bojidarka @Vikas