If I find resources for several calculations (the last one continued
for 20 days) I'll try both methods and will share You. It seems I should
find another smaller test system and reproduce the approaches.
Thank You
Sun May 20 09:55:14 CEST 2018
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I think CompEl
I think CompEl is described in the manual, the options for it are here:
http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
I've never used it, so I can't suggest anything, but you can ask on this
board for specific mdp examples.
The way CompEl works is conceptually simple: i
Dear Alex!
Yes, I thought about all Your reflections and I'm also not sure that CompEl
is well parameterzied for a non-specialist like me and the electric field
is more intuitive for me. However, when I saw the dimension 'V/nm' for the
first time, I thought that something must depend on the length
It's more of a philosophical question in, unfortunately. I don't use
CompEl, because I believe it is conceptually clunky, but that's a matter
of opinion that could turn into discussion beyond the scope of your
question. I don't study biomolecules, so I can get away with applying
direct fields.
Dear all,
Which protocol, Electric field section or the CompEl, I should use in the
situtation:
1. I built an ion channel by homology, prepared a bilayer membrane, embeded
my protein and run a simulation to relax the system (100 ns)
2. my channel was closed all the time.
3. I want to run four para
