[gmx-users] (no subject)

alex rayevsky rayevsky85 at gmail.com
Sat May 19 22:41:56 CEST 2018

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.

Thank You!

*Nemo me impune lacessit*

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