[gmx-users] discrepancy between system charge when starting simulation from a snapshot from another simulation

[Shubhangi Gupta]

Hi all,

        I am trying to simulate a metalloenzyme protein, containing zinc,
in gromacs 5.0.2 using gromos54a7 force field. The protein+zinc system has
a net charge of +1, to counter which, I am adding a chloride ion using
genion. I have simulated this water+protein+zinc+chloride system for a few
nanoseconds. From this simulation, when i take any random snapshot as pdb
file, and try to start a new simulation using the snapshot as the initial
conformation, pdb2gmx shows that the net charge on the system is -1.
However, it should be 0, as the system in my previous simulation was
neutral. I would be very grateful if someone could point out my mistake.

Thanks already,


Regards,
Shubhangi Gupta
PhD Research Scholar (YUS lab)
Dept of Chemistry
Indian Institute of Technology Bombay
Powai, Mumbai-400076.

e-mail ID: ignahbuhs.gupta6 at gmail.com
               shubhangi_gupta at iitb.ac.in


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