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

How can I utilize all the CPUs in one node during gromacs simulations?

I have installed gromacs 5.1 in server which has 4 nodes each with 40 CPUs. I am allotted to use only 2 nodes with 80 CPUs. after installation when i did sample md run only 20 cpus are being...

08 September 2017 9,639 3 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

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

How Relativistic effects is one reason for lanthanide contraction?

The Lanthanide contraction which is the decrease in ionic radii of the elements in the lanthanide series from atomic number 57, lanthanum, to 71, lutetium, is due to poor shielding of the 4f...

01 March 2021 2,272 4 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 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

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

Why initial concentration of Pb not the same as calculated one when testing using AAS?

I am currently doing research on the adsorption of heavy metal using magnetic reduce graphene oxide. I use AAS to determine the concentration of the heavy metal. I prepare the Pb solution with...

26 February 2021 9,580 4 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to search for crystal structure for material with atomic position labelled?

I am using the crystallographic open database and materials project to search for cif file but the exact structure is not mentioned or how can I deduce that the given structure and atomic position...

23 February 2021 6,723 2 View

Is this the write procedure for acid digestion of soil for heavy metal analysis using AAS?

How to do acid digestion of soil sample with 3:1 aquaregia in an open vessel?

23 February 2021 3,053 7 View