Why Runge kutta method is applied in MD Simulation (namely LAMMPS) and how can I apply 4th order RK method in LAMMPS?

More Sumaiyatul Ahsan's questions See All

How can I convert .vesta file to a .cif file?

I've used the "export data" option in Vesta software to convert my unit cell into a cif file however when I use that cif in atomsk it shows error such as "can't read the position of atom 0". If I...

28 February 2021 4,966 3 View

What are the things you should keep in mind while designing a controller for a quadrotor and want to implement it on hardware (via arducopter) ?

I am designing a flight controller for a quadrotor. At first I am designing a nested/cascaded controller consisting of only proportional controllers Kp . Now, if i tune the rate controller for 10...

03 February 2021 5,001 3 View

How to discretize a continuous time state-space model in MATLAB correctly?

I am trying to discretize a continuous time state space model using the following code s=tf('s'); G=1/(Iyy*(s^2)) Gs=ss(G) Gd=c2d(Gs,0.01,'zoh'); Now, when i use this discretized model 'Discrete...

30 January 2021 8,665 10 View

If i want to use annual time series data, but the number of observations are less then requirement, so i can convert data in quarters?

27 December 2020 7,304 19 View

Can I use conventional PCR master mix instead of hot star Taq polymerase in DNA methylation studies or in bisulphite converted DNA ?

I am trying to predict age from DNA methylation. I am using conventional PCR master mix, but I didn't get my PCR product. Is it due to Master Mix? Should I use HotStar Taq Master Mix ?

08 December 2020 8,776 4 View

How can I download Materials Studio ?

How can I download Materials Studio ? Anyone please suggest me any website. Thank you

10 November 2020 5,238 3 View

A sample size near to 20 with pre and post assessment after psychotherapy sessions. Can we apply paired sample T test? or other suggested tests?

A sample size near to 20 with pre and post assessment after psychotherapy sessions. Can we apply paired sample T test? or other suggested tests that we can apply on it?

15 October 2020 6,339 5 View

How would Universities respond during post pandemic reopening phase?

In the countries where online classes are not effectively implemented and having no possibility of taking online exams, these countries may declare reopening of universities. What measure should a...

06 August 2020 10,010 3 View

Which methodology is correct to measure Total starch content in wheat in megazyme kit?

I want to measure total starch content in wheat flour. I want use megazyme kit but I am confuse which methodology is correct for wheat because in kit there are mentioned many procedures. Kindly...

23 July 2020 190 3 View

Thermal conductivity of metallic powder?

I am doing some experiment for measuring temperature dependent thermal diffusivity and conductivity of metallic powders like inconel 718, TI6AL4V. What I observe is there is an increase, then...

15 March 2020 2,958 6 View

Energy minimization in LAMMPS using NVT ?

How do I do energy minimization in lammps with NVT ensemble ? I am using the following command and it does not seem to work. It stops at extremely high energy and gives me the error zero search...

01 March 2021 2,294 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

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

Rdf of atoms from a COM or point in lammps or VMD?

Hello all, as I understand there isn't any straight way to get an rdf of atoms from the center of mass or a coordinate of specific atoms in lammps. I wonder if anyone know any trick or way to get...

16 February 2021 2,517 2 View

How to raise temperature in small increments during equilibration in LAMMPS?

All, I am trying to equilibrate an Ice 1h crystalline structure to 250K in LAMMPS. When I tried to do this at 250K directly, the structure lost it's crystalline shape and became disordered post...

14 February 2021 5,747 2 View

Can anyone please suggest where I can find a reference for ReaxFF parameters for PTFE(Teflon) suitable for use in LAMMPS?

Trying to simulate a ice-PTFE interaction and am unable to find a reference which actually lists out forcefield parameters for PTFE-PTFE interactions using ReaxFF or even other force fields like...

08 February 2021 9,373 2 View

Should the Ice 1h crystalline structure be lost during equilibration process in LAMMPS?

I have created an Ice 1h structure and am equilibrating it 100K in NVT ensemble in LAMMPS for a timestep of 0.25fs in 3000 steps. The potential used is TIP4P/Ice. Although the simulation runs fine...

26 January 2021 9,603 11 View

How can I compute the distribution of dipole moment as a function of the angles between the dipole vector and solid surface through Lammps command?

I want to plot the distribution curve of dipole moment as a function of angles between dipole vector and solid surface in the presence of external electric field. My system is consisting a...

17 January 2021 1,508 4 View

Recognition of Molecules from a file containing molecular dynamics trajectory?

Can anyone recommend a good code/software/implementation to identify the change of molecules (bond creation/break, number of molecules at a given timestep, etc.)? I am currently working with XYZ...

12 January 2021 1,655 4 View

How can pressure commands be applied randomly in Lamps?

Hello everyone. I wrote a program in Lammps that applies pressure on three axes separately. Since in reality the pressure is applied randomly on each of the three axes; How do I write the program...

29 December 2020 7,072 1 View

Yun-Peng Wang

MD simulations deal with time evolution. For a Hamiltonian with different parts and the parts are not commutative with other, you shall use specially designed algorithm to minimizing the error while keeping the time step not too small. The Verlet and velocity Verlet are such examples. They are also called Suzuki-Trotter decomposition.