I am doing MD simulation of ag-ab complexes using GROMACS and want to know the eletrostatic potential of a surface atom in a coordinate. Please tell me if there is any method to calculate the same that would be helpful to me.
Your question is not clear, but I think you mean how to calculate the electrostatic potential at a certain coordinate R originating from certain atom r_i. If this is the case, you must take the vector difference (R - r_i), then calculate the length of that vector, call that d_i. The electrostatic potential is (1/(4 Pi e0))*(q_i/d_i). Where e0 is the dielectric constant, and q_i is the point charge assigned to atom i by GROMACS. Then you must add over all atoms you want (sum over index i).
Hello.
You can create an index file (index.ndx) with a group containing the atom you are interessed and use the command g_potential. Check the manual: http://manual.gromacs.org/online/g_potential.html
Best regards,
Ricardo Ferreira
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