Can we draw a cylindrical shape using PACKMOL?

I want to make a cylindrical shape configuration for my study using PACKMOL, can anybody suggest what would be the input file change in it if we use sphere for spherical shape. i tried replacing...

02 March 2019 5,383 2 View

In GROMACS, how to nvt equilibrate without restraints after NPT simulation with restsraints?

Hi,I am trying to NVT equilibrate without constraints after NPT simulation with constraints. but i am getting the errors in tau_t and many more. can anyone suggest what is wrong with the mdp file.

02 March 2019 7,600 5 View

In VMD, inorganic builder, hw can i build a device for a given unit cell?

while giving new material option and browse unit cell, it asked for topology file which i tried to generate using GROMACS but when i upload it and try to build device, it says non-invertible...

01 February 2019 2,029 1 View

Cannot find position restraint file restraint.gro (option -r)?

Hello everyone, while running nvt equilibration i am getting the error as: Cannot find position restraint file restraint.gro (option -r). From GROMACS-2018, you need to specify the position...

01 February 2019 9,453 1 View

Fatal error:unable to open extended system file, NAMD?

i am getting this error while running NAMD could anyone help...

31 December 2018 6,756 3 View

Charm++ Fatal error while running NAMD?

Hi Everyone, I am trying to run the NAMD configuration file but as soon as i run the command as namd2 minimize.namd > dummy.out it gives an error as: charm++ fatal error: unable to...

31 December 2018 1,415 8 View

Fatal error: Can not read file ions.tpr, this file is from a GROMACS version which is older than 2.0 Make a new one with grompp?

Fatal error: Can not read file ions.tpr, this file is from a GROMACS version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible can...

09 October 2018 6,952 2 View

Transition state doesn't seem to converge in Gaussian using QST2 although its chk point file shows the vibration for bond which would break?

does that mean reaction proceeds via SN1 mechanism or the TS doesn't exists?

07 August 2018 5,797 1 View

Is there any way to check if any transition state would exist for a reaction in Gaussian if the QST2 run fails or the reaction is diffusion controll?

Gaussian

06 July 2018 7,437 0 View

Can anyone help?This is likely either a 1,4 interaction, or a listed interc inside asmaller mol you are decoupling during a free energy calc?

Gromacs

05 June 2018 9,868 0 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

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

How to remove the residual PDMS on the silicon mold?

Incompletely cross-linked pdms are difficult to remove.

01 March 2021 798 3 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

What is Flat Lens Antenna?

28 February 2021 5,433 3 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

Why does the sum of reaction forces not match the force component of a Free Body Cut in Abaqus?

I am using Abaqus to simulate a plate with in-plane loading. The boundary conditions allow the right edge to move up and down, the displacements on the left edge are fixed. There is no rotation...

23 February 2021 711 3 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