How to interpret the RDF plots?

I have studied the structural changes of a protein in 3 different concentrations of ionic liquids (50 mM, 500 mM, and 1M). On analysis of the RDF plots, I find that the magnitude of the RDF plot...

05 October 2020 4,972 2 View

Which is the best way to find the number of water molecules around the protein?

Dear all, I am trying to calculate the number of water molecules at a distance of 0.35A from the protein. I used two gmx select GROMACS codes which have given me different answers. 1. gmx_mpi...

17 March 2020 9,117 3 View

How to get temperature contours in ANSYS FLUENT for flow over heated plate?

I am working on impingement study where air coming out of a converging nozzle is impinged on a hot plate. Plate is constantly heated using joule heating. I need temperature contours on the plate...

25 February 2019 6,673 7 View

How to interpret the RDF plot?

Hi, I am studying the stabilization of proteins using different solvents using GROMACS. Attached is the RDF of the cation (black) and anion (red) around the protein. I used "gmx_mpi rdf com rdf...

18 June 2018 7,466 3 View

Can the activity of proteins be studied using molecular dynamic simulations?

I have been studying the conformational changes and stability of proteins in different solvents using MolecularDynamic Simulations. Wonder whether changes in activity of enzymes could also be...

06 April 2018 9,153 4 View

What is the better cell line to choose for studying the effect of a particular mutation in inducing tumorigenesis: normal or cancer cell line?

I need to study the effect of a particular mutation that is hypothesized to be tumorigenic. So which cell line should I choose to study its effect: a normal cell line or a cancer cell line?

15 January 2018 2,384 3 View

Please help with geometry optimisation in GAMESS- shift in double bond

25 May 2017 2,299 6 View

What happens to the DNA from sloughed off intestine epithelial cells when extracting bacterial DNA from mouse fecal samples?

I am currently using the PowerSoil DNA extraction kit from MoBio for DNA extraction from bacteria present in mouse fecal matter. I wanted to know how the sloughed off intestine epithelial cells...

21 August 2016 5,137 1 View

Why does PBS treated with o-phthaldialdehyde exhibit absorbance at 332 nm when it is only a blank with no amine groups?

12 July 2016 8,655 3 View

mRNA to protein expression?

I have been conducting a series of experiments where I transiently transfect plasmid with my gene of interest into HT29 cells. When I performed qRT-PCR on these cell samples, I can clearly see an...

03 December 2013 6,975 8 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 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

MD MOE RMSD

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

07 August 2021 0 0 View

MGL tools

20 June 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

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

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

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

what is the simplest definition of ion exchange capacity

What this unit identifies for the ion exchange capacity ca. 0.92 meq. g-1. I am a newcomer in the membrane area. I just started. I highly appreciate your help

08 May 2021 0 0 View