Dear all,
How to prepare two mdp files for separate md 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 these two systems with -80 mV and +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 conditions affecting the opening of the pore...
Thank You!
p.s. if someone's method is suitable and give the result, I can offer a co-authority in the article containing both computational and in vitro experiments confirming an effect of a novel anesthetic's derivatives (chemisty is already published)
Dear Nebojša,
You are quite right concerning CompEL and I've already read the article You sent me, however I thought it was a modified in-home protocol (http://www.mpibpc.mpg.de/grubmueller/compel the and of the page). Well, last 7 years I didn't find any significant changes in the manual so I even didn't assume that something was changed in a such way ))))) The version I'm using is 4.5.3 or 4.6.3. it seems I should install the new one.
Thank You for the comment, concerning the first method - how should I convert a value of +40 or -80 mV into electric-field-z values, either taking into account a size of the system or the thickness of membrane, or changing other parameters (frequency, time...). It is not very clear for me, because I was and remain a little bit confused with a dimension of V/nM insted of mV. However, the second method is much more useful for the task. I'm starting reading the manual, thank You!
p.s. this is one of 20 articles I've found and read before Your advice ( Structural and Functional Effect of an Oscillating Electric Field on the Dopamine-D3 Receptor: A Molecular Dynamics Simulation Study. 10.1371 /journal.pone.016641 2) - all of them, starting from 2007 year used an el. field method. and compel is one of the latest developments that is why I didn't find in a 4.6 manual ))))))
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