Questions tagged [gromacs]

GROMACS software package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. Primarily designed for biochemical molecules like proteins, lipids and nucleic acids.

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Missing residues in ATB downloaded pdb/rtp files

I have downloaded the diglyme molecule from the ATB server (http://atb.uq.edu.au/molecule.py?molid=34570#panel-md) Two files are available: a PDB file and a topology ITP/RTP file. The name of the ...
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Large pressure fluctuations in molecular dynamics

I'm performing MD simulations, using NPT ensemble. The problem is that the pressure fluctuates severely and doesn't average at required level. For example, I set the pressure at 1 bar and it averages ...
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1answer
144 views

Analyzing MD trajectory: molecule orientation

I'm running a MD simulation (in Gromacs) of dye molecules incorporated into polymer to determine how that system responds to external electric field. There are two order parameters that are used to ...
10
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1answer
76 views

How do I calculate the radial distribution function from the centre of mass of unit cell in GROMACS?

I am simulating a droplet of water with GROMACS. The droplet consists of about 200 TIP3P water molecules and is placed near the center of a large, mostly empty box (...
11
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1answer
71 views

Unable to recreate data for benzene from paper in GROMACS 2020.5

I have been trying to simulate benzene in OPLSS-AA forcefield as per this paper: https://pubs.acs.org/doi/10.1021/ct2002122. I have been at a loss, since I believe I have everything running as per the ...
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114 views

Finding parameters for a molecule in various forcefields

Let's say I want to run a simulation for benzene in GROMACS using parameters from a certain force-field. I logged on to the Automated Topology Builder, I looked up benzene, and I found an ITP file for ...
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65 views

Error in GROMACS for adding ions to a solution

I am following Justin Lemkul's GROMACS simulation given on this website here for GROMACS. I believe I have followed the process to the T. I would like to mention that in the "Generate Topology&...
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1answer
29 views

How to overcome gromacs make_ndx automatic ranking of atomic indexes?

When working with gmx make_ndx I found very annoying the fact that atomic indexes are automatically ranked in the outputted index ...
12
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1answer
248 views

Compute RDF between COMs of two selections (or groups) using GROMACS

I have been using gromacs since years but I am always confused when I want to perform the following task: compute the RDF (radial distribution function) between the ...
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55 views

Periodic polarizable QM/MM embedding

Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
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How to effectively simulate high density systems in GROMACS?

I have a system with a dense liquid solvent and a polymer solute. I have inserted all the molecules randomly using gmx insert-molecules and then did the energy minimization and equilibration steps to ...
9
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1answer
81 views

Is there a way to understand pi-pi interactions through GROMACS?

I have two polymer molecules with benzene rings as a part of them. I would like to understand how the interactions between them influences the solvability of the polymer in a non-aqeous solvent. I ...
8
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1answer
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Generating topology for charged molecules

I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen ...
9
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1answer
199 views

Why does my calculation using GROMACS get stuck at step 0?

I have been using the HPCE on our campus for MD simulations using GROMACS. However, when I use the following script, after the job starts to run on the cluster, gets stuck at Step 0 in the log file. <...
6
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1answer
99 views

Is it possible to simulate the Raman spectra via Molecular Dynamics (MD) using the GROMACS package?

I'm new to molecular dynamics and DFT. The aim was to study the Raman spectra of a molecule in a medium. As we know the Raman spectra of a molecule change due to the induced polarization in the ...
9
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1answer
142 views

Computational biology textbook similar to “Computational Materials Science” by June Gunn Lee

I'm looking for a text for computational biology which is similar in structure to a book called Computational Materials Science by June Gunn Lee. In his book, Lee discusses the theory of MD ...
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How to do molecular dynamics calculations and analyse trajectories of small molecules? [closed]

I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is protein cofactor (FAD) small molecule (either single O2 molecule or single Chlorine atom) ...
15
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157 views

Why do interaction potential parametrizations of bulk systems not work for corresponding nano-systems?

I am studying several thermodynamics properties of crystalline iron oxides ($\ce{Fe3O4}$, $\gamma-\ce{Fe2O3}$) in their solid phases by MD simulations. At the moment, I am facing many difficulties in ...
14
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1answer
89 views

How can I decide on the order of different monomers in a co-polymer?

While performing molecular dynamics simulations on a co-polymer, how long should the minimum size of the polymer be, to replicate the experimental properties with a reasonable error? Within this ...
15
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141 views

Does anyone know any software for MD simulation which include the effect of magnetic field?

I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?
13
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199 views

How to find out the total functional form of the forcefield that is being used for a current simulation in GROMACS?

This is a doubt regarding the usage of various forcefields together in MD simulation of hydrates. For Eg., we use TIP4P/ice for water molecules, OPLS-UA for methane and EPM2 for carbon dioxide and so ...