Which software do you use for Molecular Dynamics simulation?

More Uttam Kumar Basak's questions See All

What does it signify that a system has strange attractors in phase space but its motion is not sensitive to initial conditions?

If I am not wrong, a dynamical system is called 'chaotic' if it satisfies the following two conditions: (i) having strange attractors in phase space, (ii) sensitivity to initial conditions. What...

10 November 2015 7,735 8 View

Can anybody suggest anything regarding parameterization of tetrachloroferrate (FeCl4-) ion?

I need the parameters for FeCl4- ion in any of the following force fields - GROMOS, AMBER, CHARMM or OPLS. The force field development of transition metal complexes is very difficult. I did a...

03 April 2015 5,941 7 View

Is there any model or equation for ridge dynamics?

I have a 2D system, you can think of it as a 2D sheet. There is a formation of ridges in this sheet when it is given a constant in-plane pressure. I want to model the ridge dynamics. Is there any...

06 July 2014 4,425 4 View

How can I calculate the interaction energy between two molecules as function of their separation?

I want to calculate interaction energy between two molecules as a function of their separation. I also want to see how geometry of the molecules affects their interaction energy. Can you suggest a...

04 May 2014 7,621 17 View

Is it possible to calculate the solubility of some material in water from the free energy of solvation?

I have obtained free energy of solvation in water using perturbation method with GROMACS. I want to calculate the solubility of the molecule in water. How can I do that?

31 December 2013 2,557 35 View

What if I define a dodecahedron box of a rectangular system of solvents? What will happen to the molecules outside the dodecahedron box during md?

I have solvated a ligand molecule with water molecules within a box defined by "inside box 0. 0. 0. 33.726 33.726 33.726" in packmol. Will it be meaningful and helpful to use editconf for defining...

09 October 2013 8,914 1 View

How to solvate a ligand molecule with a non-aqueous solvent like octanol?

I want to solvate a ligand molecule with (united-atom) octanol. I have a pre-equilibrated box of 512 (united-atom) octanol molecules. I am using editconf and genbox tool for solvating the ligand...

08 September 2013 8,795 8 View

Which one of the programming language do you think is better, Perl or Python?

I have used Python. It is simple and powerful. One of the crazy things about python is ipython shell. I don't know Perl. I have heard that it is an excellent scripting language. Which one do you...

08 September 2013 7,855 11 View

How can I get Antechamber working - it is giving an error message?

Antechamber from AmberTools13 is giving an error: " cannot run "..../sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit" " I have installed AmberTools13...

07 August 2013 5,264 8 View

Topology generated by ATB server contains a charge group of 32 atoms? Is it reasonable? How can I obtain the partial charges of atoms for molecule?

I have used ATB (http://compbio.chemistry.uq.edu.au/atb/) server to generate topology for piroxicam molecule (having 36 atoms). It has generated topology for GROMOS96 force field with two charge...

07 August 2013 6,827 7 View

Are there instances where molecules with larger molecular weights exhibit greater mobility than those with smaller molecular weights?

Hi, I know that low molecular weight (MW) molecules generally tend to have higher mobility, while high molecular weight molecules tend to have lower mobility. However, in my experimental...

06 August 2024 1,495 2 View

For an in-vitro drug release study, what molecular weight cut-off (MWCO) dialysis bag is required for a 117 kDa protein?

kindly reply me. Thanking you in advance.

05 August 2024 7,727 4 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

How to start a Molecular Dynamics Simulation?

Is it possible to conduct a molecular dynamics simulation to see the effects of a specific carbohydrate on the structure of lipids (e.g., micelle structure)? I am a beginner in this field and plan...

03 August 2024 3,371 3 View

Which will be the best software for the Hydration shell analysis with molecular dynamics?

I am using a windows system, what software I should use for hydration shell analysis with molecular dynamics?

02 August 2024 3,143 4 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out?

Can we patent a process flow diagram developed using a process simulator but no actual cases is carried out? For example consider a process for certain product manufacture where a new process flow...

31 July 2024 781 1 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Mostafa Eidiani Popular answer

Please see: http://www.gromacs.org/Downloads

Supriya Das

Desmond

Mohammad Ali Mohammad

Materials Studio by Accelrys (http://accelrys.com/products/materials-studio/) -- Purchase of the relevant modules is neccessary though.

Dario Corrada

GROMACS, but I would like to use/learn/puchase AMBER... By the way, in our lab we have also Schrodinger's DESMOND module on local machines, but we don't know how to run it on a cluster machine with qsub tool. Any suggestions?

Justin Lemkul

GROMACS, NAMD, and CHARMM.

Marian Butu

Gromacs, charmm and vmd

Mostafa Eidiani

Mallikarjunachari G

Materials Studio is a good software for model building, and lammps is a good software for running simulations.