How to read Gaussian Cube file?

Hi, I have a Gaussian cube file (.cube) that I obtained with gmx spatial. It represents the spatial density of cholesterol during a simulation (Protein in a membrane with explicit solvent). I...

03 April 2019 9,161 1 View

How to calculate the tilt angle of a protein (or a helix) with respect to the membrane plane?

Hi, I have a Coarse-grained simulation of a dimer with 5 transmembrane helices for each monomer and I would like to calculate the tilt angle of each monomer with the respect to the membrane...

31 December 2018 5,872 2 View

How to quantify the arrangement between helices during MD and also the effect of CHOL on the conformational changes of certain helices?

Dears, I run several Coarse grained simulations of a transmembrane protein using Martini FF. In order to do a deep analysis of my systems, I backmapped a part of the trajectory from CG to AA....

09 October 2018 4,361 2 View

How to estimate the loss in helix during MD simulation?

Dears, I run MD simulation on a transmembrane protein. When I visualised the frames, it seemed that I have some loss in alpha-helix (TM region). How can I quantify this? NB: I used timeline of...

07 August 2018 4,157 4 View

What is the lipid composition of the mitochondrial Outer Membrane (omm)?

Dear all, I would like to simulate a protein which is located in the Mitochondrial Outer Membrane (OMM). I was searching in the literature about lipid composition of this latter (in Mammals) but...

01 February 2018 5,040 2 View

How to analyzing Desmond trajectories using GROMACS tools?

02 March 2017 964 2 View

What kind of analyses that can be performed on a protein in order to study differences petween the apo and holo form during MD simulation?

10 November 2016 8,125 5 View

How to generate a topology for a HEM protein using CHARMM 27 as FF?

Dear all, I'm working on simulating a homodimer with its cofactors (hem, THG) and its substrate with GROMACS. Since my system is complex, I decided to start first with a monomere taking only...

04 May 2016 637 2 View

Fixing missing atoms and residues in PDB file before using pdb2gmx

Hello, I have missing atoms and residues in my PDB file and I need to fix them in order to proceed with pdb2gmx (GROMACS). I used swissModel but the generating file is lacking the final residue in...

04 May 2016 7,450 6 View

''Acute-Phase Proteins'' in Patients with Systemic Sclerosis

Hi every one, i need ur help please: i'm preparing my final project about the implication of autoantobodies and inflammatory proteins in systemic sclerosis and i can't find any articles about...

04 May 2011 8,273 3 View

How to compare 2 samples recruited with different sampling methods?

If I want to compare characteristics of 2 groups of patients, one group is recruited from a random sample of the general public while another group is from a sample with a fixed gender (male to...

26 February 2021 3,526 3 View

Do you consider undergoing a structure literature review / Meta analysis and getting numerical findings sort of quantitative method?

I am looking for a classification of the research methods included in literature review papers or Meta analysis ones .

22 February 2021 1,131 4 View

Can I do two kinds of mixed method in explanatory research?

Dear distinguish professors and scholars, I have a research in measuring two kinds: think tank capacity and research impact on policy. Can I do two kinds of mixed methods in order to find, "Is...

20 February 2021 6,897 1 View

How to analyse a (perceptual) study using differing/comparable sets of stimuli?

I plan on running an online perceptual experiment that has, let's say, 100 unique video stimuli altogether. Since these are too many to be rated by every participants, I would like to present the...

15 February 2021 7,444 2 View

How to analyse a split-plot design in stata ?

I have run an split-plot design experiment evaluating the efficacy of a treatment (with 3 whole plots and 4 sub-plots), and I am planning to analyse the collected data in Stata. However, I do...

14 February 2021 7,800 7 View

Can I use a likert survey for criterion sampling in a qualitative study or would that make it mixed methods?

I am doing a phenomenographic study on the reading experiences of avid v. Neutral v. Non-Readers. If I use a likert survey to criterion sample for participants, does that make it a mixed method...

09 February 2021 8,594 3 View

How to create the context-mechanism-outcome configuration (CMOc) in the realist methodology?

In the realist methodology (especially by Raymond Pawson et al), the CMOc is a common structure to explain what works, for whom, in what circumstances, and why? I'm always asked about the...

08 February 2021 2,792 1 View

Recommendations for sample size in visual qualitative research (using children's drawings)?

Hi everyone! Asking for a little help, if I may. I am working on a research project, where I aim to analyse children's drawings about Covid-19. I am fairly new to using visual data in qualitative...

07 February 2021 9,530 3 View

How do I create a categorical variable, level of exposure, and a dummy dichotomous, yes-no, variable for the Harvard Trauma Questionnaire Part 1?

I am using the Harvard Trauma Questionnaire (HTQ) Trauma Events scale (original version) that has 17 items (17 different traumatic events) with 4 response options, indicating 4 levels of exposure:...

04 February 2021 1,509 3 View

How to report path analysis / SEM with Yuan-Bentler correction from R output?

Dear all, I am currently writing my master thesis where I am analysizing my data using path analysis and SEM in R (lavaan package). Now that I like to write up my results, I am struggling with...

04 February 2021 8,993 2 View