Apramita Chand

17 Questions 15 Answers 0 Followers

Questions related from Apramita Chand

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...

11 November 2019 10,143 3 View

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...

11 November 2019 3,353 1 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...

10 October 2019 4,611 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...

06 June 2018 8,399 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?

01 January 2018 6,150 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...

08 August 2017 2,868 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...

05 May 2017 3,352 1 View

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

Is there any information regarding how to calculate hydrogen bond energy in GROMACS?

12 December 2016 3,806 2 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...

12 December 2016 2,236 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...

09 September 2016 3,330 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...

07 July 2016 7,929 7 View

What is the difference between GROMACS G53A6FF and GROMOS96 53A6FF when choosing files from an ATB server?

The file formats are different for both,when I view them at ATB site (Automated Topology Builder site). My GROMACS version shows up only GROMOS96 53A6FF force-field. Is there any difference...

05 May 2016 9,169 7 View

Why is the pressure not attaining the desired value after NPT equilibration?

In a simulation of a dipeptide in water ,I have equilibrated using Berendsen pressure coupling using the parameters given in the attached file. Why isn't my pressure reaching the desired pressure...

02 February 2016 8,540 4 View

My molecule has diffused out of the box during equilbration run in GROMACS. Should I try and center it before or after production run using trjconv?

Ideally, the molecule is centered initially and then the equilbration steps are done. Say, I've created a combined .gro file for my molecule in water and during equilbration run ,I notice that my...

02 February 2016 6,717 3 View

Is there a proper protocol on how to parametrize manually or create topology files from software for opls ff in gromacs?

I want to create a binary aqueous mixture with DMSO using opls forcefield Since a simple pdb file for DMSO coordinates won't work by input into pdb2gmx, topology files have to be created. What are...

02 February 2016 4,170 4 View

How to proceed when GROMACS shows error in residue identification while inputing a .pdb file generated by packmol

As a beginner in gromacs,I generated an initial configuration of some peptides in mixed solvent systems. After giving pdb2gmx command for generating .gro file and .top file, an error message comes...

08 August 2015 5,522 4 View

While constructing a hydrogen bond table from .lis file( platon) how can I judge which interactions within a crystal are most appropriate to consider?

We generally construct hydrogen bond tables seeing the .lis file generated from platon. However,out of all interactions within the crystal, it is necessary to include all of it in the hydrogen...

01 January 2015 1,877 2 View