How to give the pseudopotential for complex having two metal with zero and +2 charge in Gaussian?

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Modification in the input files for depicting surface (weak) ligand binding ?

Hi, we are trying to simulate ligand which is binding to the surface (exposed cavity) of a protein. The ligand topology was created from the antechamber and the complex was simulated using...

05 June 2019 961 2 View

Why the polynomial equation (including quadratic equation) is not so popular in QSAR modeling?

Studies have shown that quadratic equation gives improved correlation coefficents than linear equation. Still, Linear correlation is more popular amung the modeling community. What are the...

11 December 2018 4,161 3 View

Is the cpu load and processor affect the molecular dynamics simulations results?

If I simulate the two similar systems with similar parameters under different CPU load and nodes/processors. Then, will I get the replicate results ? I am asking this to be ensure as I am going...

05 June 2018 6,824 4 View

Is there any visualisation software that can display detailed protein-protein interactions?

I have docked two protein in order to comprehend the residue involve in PPI interaction. Now, I want to visualise detailed interaction types and bonding pattern. I have tried Discovery studio,...

10 November 2017 2,509 7 View

Modelling of ionic supramolecular complexes ?

I am interested in studying the dynamic behavior via MD simulations by utilizing the benchmarked OPLS force field. In this course, I have fired various calculation with QM optimized structure...

04 May 2017 2,324 2 View

How to give the input for oxidation state of the metal in Gaussian?

while optimizing host-guest complex in GAUSSIAN at any level, we have the option of only mentioning overall charge on the system not on a particular atom. In such case, if I want to represent the...

04 May 2016 1,503 7 View

X-ray coordinates of pdb

where to find the X-ray coordinates of a particular protein deposited in RCSB Protein Data Bank (PDB).

08 September 2015 9,246 1 View

Molecular Dynamics simulation of a protein (2FOM) with larger RMSD fluctutation ?

Hello Everybody ! I am trying to perform MD simulation of a protease apoprotein (pdbid: 2FOM) as well as its complex with inhibitor. Upon analyzing, I found that there are huge fluctuations in...

01 January 1970 9,653 4 View

What is the production process of CaFe ferroalloys?

I looking for ferro calcium production process

03 March 2021 1,755 4 View

How Relativistic effects is one reason for lanthanide contraction?

The Lanthanide contraction which is the decrease in ionic radii of the elements in the lanthanide series from atomic number 57, lanthanum, to 71, lutetium, is due to poor shielding of the 4f...

01 March 2021 2,272 4 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

Why is the sum of the elements in a row in a Q matrix equal to zero?

When explaining substitution models, the substitutions are expressed as Q matrix. Why is the sum of the elements in a row zero?

28 February 2021 3,864 3 View

Can water be extracted from Olivine?

I have always been interested in geology and wondered about how unique structures of materials behave in different circumstances. I stumbled upon Olivine, the magnesium iron silicate, and heard...

28 February 2021 7,330 4 View

How does charge on working electrode changes with rising potential?

During performing CV of a GCE or modified GCE, we rise the potential in the first half of the cycle and reduce it in reverse half. During the first half, what is the nature of charge on GCE or...

25 February 2021 7,994 3 View

Why the CHi^2 is close to zero with a bad fitting but the Rp and Rwp are still high?

I am refining my XRD data using in FullProf program. The intensity of the modulated X-ray peaks is almost flat. I tried to adjust the peak intensities but unsuccessful. What is the reason? I guess...

23 February 2021 2,304 4 View

Can we use a compensation matrix with single staining that the negative population for each single staining is below zero?

Recently we used single staining to make a compensation matrix. But, for each single staining we saw that 13 to 25 percent of our negative population had been shown below Zero. In this situation...

21 February 2021 9,982 2 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

What is the detection limit of ED-XRF technique for transition metals in silicon ?

Hi everybody, please, can someone tell us if the transition metals (W, Fe, Ni, etc ...) in silicon destined for solar cell manufacturing can be detected by ED-XRF technique. Note that the...

18 February 2021 6,231 4 View