I am learning MD simulations using GROMACS and while I was doing a protein in water MD simulation a doubt raised. I was following the steps mentioned on the tutorials page and it said The system has to be neutralized by adding ions using "genion" module of gmx and the reason given was " Since life does not exist at a net charge, we must add ions to our system", but most of our biological systems in the physiological level exist in charged states was my understanding.
A little more explanation for this step would be helpful in understanding the reason behind the step.
will running an energy minimization step in a charged state of the system,affect the run ?
Dear Kumar,
the reason for neutralizing the system is the use of Ewald summation (usually implemented as particle-mesh Ewald (PME)), for computing long-range electrostatic interactions, which formally requires charge neutrality of the molecular system for accurate calculation. For a system with a net charge, the Ewald algorithm implicitly introduces a uniform background charge distribution to neutralize the simulation box, but this (usually) doesn't reflect the distribution of ions in the systems, leading to artifacts.
This paper Article Quantifying Artifacts in Ewald Simulations of Inhomogeneous ...
provides deep insights into this problem and possible solutions.
Best regards
Johann
Compare the results obtained with zero and non-zero net charge: If there is a difference, the net charge matters; if there is no difference, the net charge does not matter.
Dear Kumar,
the reason for neutralizing the system is the use of Ewald summation (usually implemented as particle-mesh Ewald (PME)), for computing long-range electrostatic interactions, which formally requires charge neutrality of the molecular system for accurate calculation. For a system with a net charge, the Ewald algorithm implicitly introduces a uniform background charge distribution to neutralize the simulation box, but this (usually) doesn't reflect the distribution of ions in the systems, leading to artifacts.
This paper Article Quantifying Artifacts in Ewald Simulations of Inhomogeneous ...
provides deep insights into this problem and possible solutions.
Best regards
Johann
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