Wojciech Szlasa

7 Questions 13 Answers 0 Followers

Questions related from Wojciech Szlasa

How to monitor cholesterol content in the cell membrane?

I am looking for a simple and low-cost method of monitoring the cholesterol content in the cell membranes. My initial idea was to stain them with cholera toxin (anti-GM1 ganglioside) to get...

11 November 2019 9,443 1 View

How to understand that one system does not work in simulation under the same protocol as the others that work?

I am simulating electroporation in varying cholesterol content in the lipid membrane. I am trying to simulate each system exactly in the same conditions and with the same protocols, but the system...

08 August 2019 7,069 6 View

Why the manual change of ion position makes and error in the simulation?

For a long time I am dealing with a problem with MD simulation. I want to simulate a system composed of a lipid bilayer with two separated "baths" of water with ions inbalance. My protocol works...

08 August 2019 1,768 3 View

How to convert coarse graine model of lipid membrane into atomistic?

I have prepared a simulation of rafts formation in the membrane using Martini force field and now I am trying to convert it into atomistic model for further research. However, I have a problem,...

08 August 2019 7,014 2 View

How to merge two .pdb files into one?

I have a model of a membrane (256 lipids per layer) and I want to multiply the .pdb file 4 times to create a bigger membrane (1024 lipids per layer). I know how to multiply and align the replica...

08 August 2019 1,358 6 View

Setting constraints = none in minimization simulation, is it a good idea?

I have performed a long MD simulation of lipid rafts formation using MARTINI force field. After that I have converted the system to atomistic model (using built in CHARMM-GUI converter). After...

08 August 2019 6,423 3 View

How to insert a trans-membrane protein into the already build membrane system without preparing it from the very beginning?

I have build a very complex membrane system, which I would like to use for MD simulations with GROMACS. I have made some calculations with it and I have come to the idea, that I have to insert a...

01 January 1970 1,769 9 View