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

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

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

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

11 December 2016 3,598 2 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

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

Why does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 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