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

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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...

10 November 2019 9,364 1 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...

07 August 2019 1,686 3 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...

07 August 2019 6,345 3 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...

07 August 2019 6,990 6 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...

07 August 2019 1,213 6 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 1,680 9 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

Arena simulation - how do i model the following model in ARENA (see description) (new to ARENA)?

Hello, I'm fairly new to ARENA and I have the following problem: I have two queues in which, in each queue, a different order type arrives (both having an arrival rate of exponential 10). Order...

02 March 2021 2,431 3 View

Is there any test to determine the cardiovascular risk of patients with obesity? from the perspective of obesity?

We found tests to determine cardiovascular risk taking into account lipid profile, blood pressure, age, history of diabetes, other laboratories. But when weight is involved, there is a paradox. I...

02 March 2021 6,036 1 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View