How can I correct my electrostatic potential figure to be symmetric?

10 November 2020 1 7K Report

hi.

I have done electrostatic potential analysis on a symmetric bilayer contains 10% Cholesterol but I've got this figure and I thought there is a problem with that as the potential is not symmetric and it is not equal in the both leaflets.

I will be thankful if you could help me solve this problem.

Nazanin Nafisi

Wojciech Kopec

thank you so much.

I just did not know about "-correct" option.

Badges
Science topic

More Nazanin Nafisi's questions See All

Hello everyone, I am doing an online survey through online panel of Amazon Mechanical Turk. how I can find a sample size formula not to be old?

I used Cochran (1963) sample size formula, but as it shows it so old and my advisor asks for some new references for finding an appropriate sample size.

01 February 2021 8,275 4 View

Does anyone know any article on free convection heat transfer from an oblate with uniform heat flux?

Does anyone know any article on free convection heat transfer from an oblate spheroid with uniform heat flux? All articles I've found are about isothermal oblates.

14 December 2020 1,163 4 View

How can I simulate electroporation for a bilayer?

hi I am trying to simulate electroporation for a bilayer containing 10% cholesterol on GROMACS. I have read lots of articles but the only parameter that they have talked about was the electric...

15 November 2020 7,602 2 View

How should I make an index for gangle in GROMACS?

Hi. I'm analyzing a bilayer and I want to make an index for calculating tilt angle. my problem is I have no idea about how to create such an index which contains vectors in it. I would be...

01 October 2020 9,021 1 View

How can I build a DMPC bilayer contains certain numbers of Cholesterol molecules on GROMACS?

Hi. I'm new to GROMACS and I want to simulate a DMPC bilayer contains 8 Cholesterol molecules. But I have no idea about how to add Cholesterol molecules to my simulation box.

07 July 2020 5,699 1 View

How can i resolve the size of nested-multiplex pcr?

Hi there, I have a problem to get a conclusion in my PCR results. I have nested-PCR product in which the first run size is what i expected to be. However, the second run is ~100nt larger than...

21 September 2018 3,901 5 View

How to optimize periplasmic protein expression in E.coli (BL21)?

I want to optimize protein purification. My protein is expressed in periplasmic space of E.coli. I particularly want to know what is the routine protocol for these kind of proteins. Is it 1mM...

16 July 2017 5,042 7 View

Whats are the usage of isochornal annealing of metalic glass?

13 May 2017 1,335 2 View

High power density for the Pt/C cathode?

09 September 2016 2,316 1 View

What can I add to the fish cell culture medium to improve cells situation?

17 June 2016 6,540 7 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

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 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

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View