Water flux inside a pore?

Hi all, I am performing a Molecular Dynamics simulation of a water pore inside a membrane. I am experimenting with some analysis options and I am having a bit of a trouble understanding the water...

01 February 2019 8,849 2 View

Trouble with gmx distance?

Hi, I am trying to calculate the distance between two atoms, which are defined in an index file. The command that I use is: "gmx distance -f output.gro -s prod.tpr -n index.ndx -oav...

07 August 2017 3,238 4 View

Problem running heme proteins on gromacs?

Hi I am trying to simulate a protein containing a heme, using Gromacs and Charm27 force field. When I try to run pdb2gmx I get an error. I have looked the force field directory and found that this...

09 October 2016 2,942 2 View

Temperatures for Replica Exchange Simulations?

Hi, I am trying to simulate a protein using Replica Exchange. By reading at the literature I found what values are needed as a Tmin, Tmax and also the number of replicas. Apart from that there is...

07 August 2016 7,329 1 View

Paper for Replica Exchange MD?

Hi I want to perform an remd simulation of a large protein system. The bibliography I found so far is about small systems and doesn't describe the way they decide on the number of replicas or the...

07 August 2016 3,321 8 View

How to calculate bond force constant for CLA for molecular dynamics ?

I am using Gromacs and I want to edit the ffbonded.itp in oplsaa.ff directory. I have by literature the bond length but I can't find the force constant. Is there a way to calculate it?

05 June 2015 1,829 5 View

Any advice on my problem adding new molecule in aminoacids.rtp - gromacs?

04 May 2015 8,571 4 View

How can I proceed with a molecule.itp in Gromacs?

I have made a molecule.itp file according to the chapter 5 of Gromacs Manual and existing entries in the ff directory I want to use.My problem is that I don't know how to continue, in theory I...

04 May 2015 5,387 3 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

How the parameters (such as Mw, Chemical bonds, polymer bland and so on) affect the mechanic property of polymer (such as storage, loss modulus) ?

Anyone can recommend any books on such topics? Thanks in advance.

02 March 2021 8,457 2 View

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View

How can you bring two structures together to create an adhesive bond in LAMMPS?

I have created an Ice 1h crystalline structure and an Aluminium substrate structure and equilibrated both at 250K. Now I need to bring them together in a way that an adhesive bond is created....

01 March 2021 3,325 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 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

I am looking for a simple software program to model 3D chemical bonds. The purpose is to generate high-quality graphical abstracts. Any suggestion?

Hello everyone: I am looking for a simple software program to model chemical bonds. The purpose is to generate a high-quality graphical abstract for a top leading journal in the field of...

23 February 2021 8,012 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