Is there any way of calculating hydrogen bond energy in GROMACS?

More Apramita Chand's questions See All

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 3,428 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 10,226 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 4,677 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 8,453 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 6,218 3 View

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

I've carried out a 100ns simulation of protein in water and want to calculate hydrogen bond (forward) lifetime between Protein-Water. I tried g_trjconv with application of -pbc mol -ur compact...

07 August 2017 2,934 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 3,407 1 View

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

In gromacs ,on using -life option we get the following answer Type Rate (1/ps) Time (ps) DG (kJ/mol) Chi^2Forward 0.149 6.692 9.313 0.00998919Backward 0.589 1.699 5.894One-way...

11 December 2016 2,318 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 3,392 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 7,976 7 View

How to develop investments in renewable energy sources?

08 August 2024 5,112 3 View

Is it possible to plot the atom-projected band structure using GPAW?

Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...

07 August 2024 269 3 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Why results of ROS flurescence are negative as there was no bacteria within?

Hello. I am working on ROS production of two systems: system A is cerium oxide and hydrogen peroxide, system B is cerium oxide nanoparticle, hydrogen peroxide and potassium bromide. I did some...

04 August 2024 5,974 3 View

How to Transform my handy-wavy explanation of why group I/II metals oxides in aqueous solution are basic into a rigorous argument?

I heard an explanation about something being a better proton acceptor or lone pair donor but that doesn't make sense. I couldn't explain in in terms of acid-base theory. The hand-waving way I saw...

03 August 2024 9,918 0 View

What is the ionic radius of Hydrogen anion? And how to know the exact ionic radii of the elements?

I'm trying to calculate the tolerance factors of the hydride perovskite and the value calculated by me and the reported values are contradictory. Need more clarity in using the correct ionic radii...

01 August 2024 2,614 1 View

Is artifacts in XPS possible to build high deviation in binding energy larger than 5 eV??

Hello. Thanks for your consideration to see my question. Recently, I conducted XPS anaylsis of g-CN that is prepared from thermal polycondensation of DCDA, so-called conventional bulk-g-CN,...

30 July 2024 9,824 2 View

How to make the concentration measurements for the hydrogen absorption/desorption in the metal hydride?

Hello Everyone! I am trying to create a metal hydride system where I am trying to create a temperature control with the emphasis on measuring the concentration of the hydrogen with the hydrogen...

29 July 2024 7,577 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

Is there a database with onshore wind production for the wind farms in Portugal?

I am looking to predict some production for future onshore wind energy production in Portugal, is there any database with info of performances of the existing wind farms in the country? something...

28 July 2024 1,750 1 View

Nikhil Maroli

see this

https://www.mail-archive.com/[email protected]/msg51347.html

I was wondering what you are going to do after knowing the hydrogen bond energy.As far as I know there are no direct methods in Gromacs, same for hydrophobic interaction energies.

There is tool available, MDanalysis python package or try in YASARA which will give hydrogen bond energy at particular structure -not over time.

Lakshmikumar Kunche

There is an indirect way. No of hydrogen bonds between solute and solvent can be found in gromacs. In a paper by berendsen et.al, they have mentioned that HB energy of one HB for a particular water model. for SPCE model it is -30 KJ/mol. Multiply this value with No.of hydrogen bonds you will get HB energy.