How To Run Sander.MPI which doesn't seem in AmberTools18 package?

I installed AmberTools18 and I installed MPI libraries as well. Everthing is working but when I want to run sander parallel like this: mpirun -np 32 sander.MPI -O -i min.in -o min.out -p...

06 July 2019 4,514 6 View

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I am trying to let's say BH3 imroper force constantsfor Amber force field. Normally scan dihedral angels and obtain values I want. But As far as I know, Gaussian is not capable of using...

31 December 2018 5,749 4 View

How to Calculate Lennard-Jones Parameters from TDDFT?

I am trying to develop parameters for AMBER FF and calculate Lennard-Jones parameters for Fe+3 ion. I really did a deep search and I found that it is the best way to use TDDFT for this with a high...

31 December 2018 3,073 2 View

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02 March 2018 4,662 2 View

How to Convert Gaussian Angular Force Constants units to kcal/mol/radian^2 units?

Hi, in gaussian FTIR log file, all force constant units are mdyne/A. It doesn't matter for gaussian the vibration belongs to bond or angle it uses the same unit. But Amber gaff file uses...

02 March 2018 980 3 View

In VEDA Software Which Vibrations Are "Asymmetric" or "Symmetric"?

02 March 2017 7,698 4 View

What analysis to choose with a large neste dataset and clearly skewed or kurtotic distributions?

Hello! I have a dataset of n=3000 nested within 8 countries with approximately 200 or 400 responses in each country. I originally planned to perform multilevel modelling with 4 dependent variables...

02 March 2021 6,865 1 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

What is Flat Lens Antenna?

28 February 2021 5,433 3 View

How do you mesh a thin solid in Fluent?

Hello, I have used the shell function on SpaceClaim to create thin solids for the model I am studying. These are contained within an enclosure for my study. I chose this approach as it avoids the...

24 February 2021 8,856 3 View

Are there any candidates for an Einstein's bare cosmological constant?

It is commonly accepted that General Relativity has its own 'bare' cosmological constant that contributes together with the cosmological constant resulting from vacuum energy density for an...

23 February 2021 5,448 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 resolve Gaussian error termination " Error termination via Lnk1e in F:\G16W\l103.exe" for TS(QST3)?

When I run the job for TS(QST3) in gaseous phase, it was completed without any error. But when I add water in CPCM model it terminated with an error: Inconsistency: ModMin= 2 Eigenvalue=...

21 February 2021 3,198 2 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

How to calculate the Atomic Polar Tensor using DFT ?

Dear friends, I am a beginner at DFT calculation. I have done a structure optimization using DFT- B3LYP/6-31G*, Nevertheless, I don't know How to calculate the Atomic Polar Tensor (APT) in...

17 February 2021 9,082 3 View

I want to simulate a system containing protein and heavy metals; which force field is most reliable for this purpose?

The protein I want to simulate has multiple heavy metals. I wanted to know which force-field I should use with GROMACS to achieve this. Most importantly, do the latest updates in the force-field...

16 February 2021 2,420 1 View