[AMBER] Few queries about membrane protein simulations

From: anu chandra <anu80125.gmail.com>
Date: Mon, 8 Jun 2015 15:45:18 +0100

Dear Amber users,

Though I have been using Amber for protein simulations, I am here trying to
use Amber for my membrane protein simulations. Since I am new to membrane
protein simulations, I would like to get your suggestions for few of my
quires, which will helpful for me to set the simulation on.

My queries are,

1. I wish to use lipid 14 and FF14SB force fields for membrane and protein
respectively. Will it be okay? Do I have to use any correction terms here?
I will be using POPC membrane.

2. I have noticed in literature that , for microsecond long simulations,
sometimes a 3 fs or 4 fs time steps were used. How safe to use such a large
simulation time step, though it reduce the use of computations resource?

3. The membrane protein, I am working with, transport ions depend on the
concentration gradient. In order to implement this in my simulation, I am
planning to add ions ( for e.g KCl) in one of the leaflet to see the
movement of ions to the other leaflet through the pore. Am I making sense
here, by restricting ion distribution to only one of the leaflet rather
than randomly placing in the entire simulation box (usually do for protein
simulation) at the starting of simulation?

4. How can I build slab geometry boundary condition in Amber to maintain
ion asymmetry? (http://www.ncbi.nlm.nih.gov/pubmed/12829468)

5. If I would like to do membrane protein simulations with an applied
electric filed along Z-direction, how can I implement the electric field in
Amber simulations?

6. Is it possible to do PMF calculation with classical MD trajectories or
do I want to carried out umbrella sampling separately for PMF?

7. Though I wish to use Amber for membrane protein simulation, some one
kindly provide some reference for membrane protein simulation where Amber
used? ( sorry, I couldn't get one)

Many thanks in advance
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Received on Mon Jun 08 2015 - 08:00:03 PDT
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