Gaussian cub output is not overlapping with isosurface ?

I want to do Bader charge analysis and I have observed that the cub file generated from gaussian have problem in overlapping to its surface when opened in Vesta. any suggestion what could be done...

07 August 2018 2,181 4 View

How to design hairpin model structure for DNA

I want to simulate hairpin DNA with drug complex, but I found it difficult to design pdb file for hairpin DNA. I tried few available online resources but can not design, the sequence I am using is...

07 August 2017 2,324 7 View

Interaction energy from md trajectories.

I used namdenergy plugin in vmd to extract total, vdw and electrostatic energy. I am confused to know about the energy provided by apbs/mmpbsa. How it is different from the data obtained from...

09 October 2016 3,405 3 View

How can I build model for coarse grain simulation for graphene?

I want to build graphene coarse grain system. I tried CG builder, but for CG builder I need initial pdb, that I tried to build using VMD nanotube builder, I can build the model, however when i...

04 May 2016 2,001 5 View

How to make double stranded cDNA from single stranded cDNA?

03 April 2016 5,477 8 View

What kind of raman shift could be observed from peptide?

I had a peptide, I am trying to get raman spectra of peptide, I found in literature, the shift in peak could be observed. What kind of shift could be observed red/blue and Why? I had done some...

09 October 2015 4,447 5 View

How do I calculate the number of close contact and contact area between receptor and ligand?

02 March 2015 2,836 7 View

Can we do umbrella sampling and SMD by CHARMM or NAMD?

I want to do Umbrella Sampling (US) using NAMD, my confusion is as follows: 1. US can be perform using SMD, therefore, how to decide the SMD config file input is correct or not? What input CV or...

10 November 2014 5,450 3 View

Can anyone help me to design a new force field for a small organic/inorganic molecule for NAMD?

06 July 2014 8,981 16 View

If we want to know the result output from a NAMD simulation, what different results could be obtained?

I am new to NAMD and recently run a simulation of DNA-organic molecule interactions in NAMD for 20 ns. I want to know what the different results are that I should analyze using the output of the...

05 June 2014 1,975 6 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 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

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

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View