Dear all, How to modify a mdp file to generate two different tpr files, from the same initital coordinates of a Na 1.5 voltage gated channel in the membrane (it is already relaxed and in a closed state)? I need to set parameters for the system with a voltage of -80 mV and than, after 100 ns start it with a voltage of +40 mV. As I understoond it should be distributed along Z-axis but I don't know how to deal with correspondent three values in mdp in the elecric field section and how to assign a side with a higher or lower potential (to choose a correct direction for ion permeability). It seems that it should look like this: """ ; Electric fields ; Format is number of terms (int) and for all terms an amplitude (real) ; and a phase angle (real) E-x = ' E-xt = 'not implemented' E-y = E-yt = 'not implemented' E-z = 1 4 0 or 1 -8 0 E-zt = 'not implemented' """ the first : only 1 is implemented (with frequency 0) so enter 1, the second : the strength of the electric field in V nm-1, the third : any number here since a cosine of frequency zero has no phase. """ The reason for such manipulation is investigation of inhibitory conditions affecting the opening of the pore...I didn't find any tutors on the theme. Of course, I could start the md and then tune the mdp file, but the system is about a half of a million atoms and it will take too much time.
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