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 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

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

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

Does the pressure(-600 mmHg) affects pH?

When I conducted the degassing experiment using decompression under anaerobic condition(and I used ferrous based chelating agent), the oxidized ferric were observerd. So, could you tell me the...

03 March 2021 4,892 5 View

How optimize the Size Exclusion Chromatography?

Hello! I'll do a size exclusion chromatography, but I only have an open column, and I'll perform the peptide extraction from yeast, using buffer lysis (sodium phosphate 50 mM/NaCl 30 mM/DNAse and...

01 March 2021 2,215 2 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

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

Which database would give me this list of chemical components?

Dear colleagues: I would like to know if anyone knows of a database that gives me the parameters pH, K, K, Mg, P, C, N, Zn, Cu, Ni and Cd of common foods. I find a lot of information of proteins,...

26 February 2021 5,525 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

Why is NH4OH added in heavy metals limit test?

The limit test I'm referring to is USP method II. In this procedure you need to dropwise add 6N of NH4OH to the sample until it the pH is alkali. After that you need to dilute and add HOAc until...

23 February 2021 2,049 3 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

Is there an ideal incubation time of RGO-modified SPCE before subsequent use, i.e., electrochemical characterization or further modification?

I notice that upon washing and air-drying of my RGO/SPCE surface and characterizing again via DPV, the current response towards ferricyanide probe significantly decreases. My worry is that the...

22 February 2021 5,324 3 View