How to incorporate the KBFF urea model into a force field in GROMACS package?

The KBFF or Smith urea model is widely recommended for simulations. It has some particular parameters as outlined in the paper attached and it follows the geometric combination rule. In an...

10 November 2019 3,246 1 View

How do you define inter-peptide and intra-peptide contacts/hydrogen bonds in a multiple peptide simulation?

In GROMACS, for calculation of inter-peptide hydrogen bonds, on choosing 'Protein' option twice from the index file (after the gmx hbond command) would give both intra- and inter- peptide hydrogen...

10 November 2019 10,016 3 View

How to implement specific solute models in GROMACS force fields?

In simulations, we often use solutes like urea or TMAO and there have been various differing models for these. For instance, in urea we have the Smith models ( for KBFF as well as the one for...

09 October 2019 4,520 4 View

How to calculate preferential interaction coefficient between protein-water/cosolute from GROMACS trajectory?

I want to calculate the preferential interaction coefficient and subsequently the Gibbs free energy of solvation for protein in water and in water-co-solvent mixture. According to the equation...

05 June 2018 8,309 1 View

Is it possible that short peptides may adopt compact conformation in urea solution and extended form in presence of protecting osmolyte?

Contrary to established research,is this kind of opposite behavior possible? Any literature on this? Any ideas how this can be possible?

31 December 2017 6,085 3 View

Hydrogen Bond Lifetimes calculated in gromacs with and without applying pbc are different. Which value should be considered?

07 August 2017 2,674 4 View

Problem with center-of-mass RDF and subsequent coordination number calculation in GROMACS

I want to calculate the COM RDFs between my peptide and water for which I have used the -com option in gromacs.(Also tried with -com and -rdf res_com). It generates a wierd RDF which does not look...

04 May 2017 3,253 1 View

What is the correct way of calculating hydrogen bond lifetime in GROMACS?

11 December 2016 2,067 7 View

Correct way of calculating diffusion constant through velocity autocorrelation in GROMACS

I want to calculate the diffusion constant of urea in my system from Velocity Autocorrelation Function using GROMACS. So I used the commands:g_velacc -acflen 1001 -nonormalize -mol -n index.ndx -s...

08 September 2016 3,228 5 View

How can I build caps of the amino acid residues of my peptide (downloaded from RCSB) so as to incorporate into GROMACS?

I want to cap the ends of my peptide chain. Though -ter option of pdb2gmx takes up its zwitterionic form quite easily, I've read somewhere that termini are quite mobile and it is better to proceed...

06 July 2016 7,708 7 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

What is the best way to keep an anaerobic chamber anoxic in the absence of hydrogen?

I'm a graduate student who works with an anaerobe, so I often work in an anaerobic chamber. I've been working on an assay that involves the steady-state of the quinone/ quinol pool. Anoxic...

03 March 2021 2,971 1 View

After a reference from Int J Body Compos Res, can any body help?

Hi, I am after the reference below, my library says it cannot obtain a copy either locally or internationally, any help appreciated! Chris Wang ZM, Heshka S, Wielopolski L, Pi-Sunyer FX, Pierson...

03 March 2021 6,193 1 View

Irradiation data for JAPAN?

Hi, Could you help me to get the latest (2019, 2020) solar resource data for a particular site in JAPAN? PV GIS and NSRDB data are not in reach to JAPAN, I'm looking for some other database for...

03 March 2021 961 3 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Can polymer concentrations be calculated based on the number average molecular weight?

Hello, I spin-cast two different polymers onto wafers and measure their height as a function of initial concentration. For polymer A, I have the weight-average molecular weight (Mw) as well as...

28 February 2021 7,882 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 to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 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

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