How to analyze root mean square inner product (RMSIP)?

Hello all, I have generated a MD simulations data with triplicates and now i want to analyze the similarity between the replicates using first 10 eigen vectors. I have preformed PCA...

06 July 2018 6,386 0 View

How good to use triclinic box for gormacs simulations?

I have performed simulations for Protein RNA complex around 1500 residues. I have used triclinic box with 1.4 nm distance from the edge of the box to protein as triclinic box takes less number...

09 October 2017 1,429 1 View

How to consider protonation states of histidine in Gromacs simulation?

08 September 2017 223 1 View

Any suggestions on generating ligand toplogy using OPLS all atomic force field compatabile to gromacs?

I am currently working on drug complex, i am using OPLS-AA force field, i have to generate a topology file for ligand compatible to gromacs using OPLS-AA. any suggestions please... Thanks in advance

05 June 2015 5,768 2 View

How do you replicate the number of lipids in bilayer for membrane dynamics using gromacs?

03 April 2015 8,994 5 View

How can I rename the lipid.itp file in order to match gromos53a6.ff for membrane dynamics using gromacs?

03 April 2015 5,217 3 View

Using 20 frames (each 5ns ) from 100ns are reliable to calculate binding free energy calculations?

I wanted to calculate binding free energy calculation of my complex (protein +inhibitor). I have no resources to calculate for large number of frames (ie, 5000 frames from 100ns) hence I have...

09 October 2014 3,536 10 View

PCA and NMA approaches on MD simulation trajectory is same?

I have done 100ns simulations for my protein using gromacs, and then subjected to PCA analysis from gromacs (g_cova, g_anaeig). In order to see the dominant motion within the proteins (WT and...

05 June 2014 5,544 4 View

How reliable is the average structure of trajectory from gromacs simulation

While taking the average structure from GROMACS simulations of a complex, which average structure is reliable? For example in GROMACS there are three options ox (average), oq(bfactor) and...

05 June 2014 7,990 1 View

What are your suggestions on my unphosphorylation approach?

In order to construct unphosporylate kinase, I have replaced phopothreonine with threonine from active crystal structure computationally, as there is no inactive crystal coordinates for my kinase....

04 May 2014 5,924 0 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 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

I got 02 moderator values defining Johnson-Neyman significance regions. Is it an error?

Hi everyone, I am conducting research for my Master's thesis. I am using PROCESS by Johnson-Neyman to analyze my Moderator model. I test the relationship between Public Service Motivation and...

03 March 2021 2,350 2 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

PACYC PCR not working after several attempts. Would anyone have any suggestions?

So, I have been trying to run a pACYC PCR which will be used later on for a Gibson Assembly. However the PCR is not working. I have already tried gradient PCR and changing extension time; however...

02 March 2021 1,146 2 View

What SPSS analysis should I run with one IV (with two levels) and two DVs?

Hi, I am trying to figure out which test would be most appropriate to run for the following question: Is there a difference in task blood pressure between smokers and non-smokers? There are two...

01 March 2021 8,235 2 View

OpenBCI eeg--has anyone used them?

I'm looking to try out an off-the-shelf EEG set for some exploratory work. Curious if anyone has used the OpenBCI, and how much set-up work is required. I've heard they are more difficult to get...

01 March 2021 4,128 3 View

Is there any expert in Smart PLS who can help me?

Dear colleagues, I have a manuscript that needs an expert in smart PLS to run the analysis, Is there anyone expert and ready to help me, please?

01 March 2021 8,212 3 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View