Hello all,
i am working on a protein complex. For a certain analysis, i am trying to add ethylene molecule in system (Protein + water), to check the variation in system. I have inserted 10 molecules of ethylene by using genbox command (specifically -ci option ). The system generated by these steps is minimizing properly, also equilibriating properly. But when moving on MD run it is showing error of particles communicated to PME node more than a cell length out of the domain decomposition cell of their charge group/ 1-4 interaction not within cutoff. Generated output is showing that inserted ethylene molecule are not settling in system properly and shuttling out from the system. I guess this the main issue, how ever kindly help me in troubleshoot.
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.
@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
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