[gmx-users] -rerun input trajectory for calculating electrostatic energy

Apramita Chand apramita.chand at gmail.com
Thu Jun 14 13:46:21 CEST 2018

For calculation of electrostatic energies between protein-solvent from
gromacs as proposed by Lindgren et al, in the paper "On the stability of
chymotrypsin inhibitor 2 in a 10 M urea solution. The role of interaction
energies for urea-induced protein denaturation",

the -rerun facility of mdrun has been used using mdp file optiond for
cut-off scheme rather than PME.. What is the trajectory that has to be
supplied to the -rerun flag? The equilibrated trajectory for production run
all over gain or the final trajectory run after production run from the
previous simulation done using PME?

Thanking you,
Yours sincerely,
Apramita Chand

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