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12:41 AM
3
Q: LEED - determining surface structures

LeifHow can one describe surface structures (before and after adsorption)? I understand the diffraction theory but I have never really tried to determine the structures of samples by myself. LEED (low electron energy diffraction images of Pd(1,1,0) surface (clean and with adsorbed CO): All I can se...

 
 
4 hours later…
4:25 AM
0
Q: How to "draw" a coordination bond (dashed bond) in MOLFILE?

Gunther SchadowHow can we "draw" a coordination bond (dashed bond) in MOLFILE? I cannot find a bond property or option that would allow me to choose such a thing. So many drawings of organo-metallic compounds (e.g., metal ion and chelator) contain that. How come the MOLFILE format doesn't support such a thing?

 
 
3 hours later…
7:46 AM
posted on September 16, 2021 by /u/Well_Why-Not

Thing I want to do - Simulated Annealing of a Polymer Methodology I am following - Create a Polymer chain of desired length. Use PACKMOL to pack desired number of chains in a conveniently huge box. Using LAMMPS follow the general equilibration protocol, NVE, NVT, NPT dynamics. Shrink the box size using NPT dynamics to get desired density. Output density using 'thermo_style cust

 
 
5 hours later…
12:37 PM
posted on September 16, 2021 by /u/Temporary_Scar8023

I am trying to simulate a silica slab in gromacs. For that I have to generate the topology for the slab. I referred to the gromacs forum where I was told to use the x2top command to generate the topology for a periodic system. But the problem, when I ran the command with the suitable atom types in the atomname2type.n2t file, but I got a error where forcefield was not found for some of my atoms

 
 
1 hour later…
1:44 PM
0
Q: Spin contamination and expansion of unrestrict determinants

AlfredVI was studying with the book "Modern Quantum Chemistry" of Sazbo and Oustland. In the chapter 2, they talk about unrestrict (UR) determiants. It's explaneid that UR determinants are not eigenfunctions of $S^{2}$, but we can expand them as linear combinations of singlet $|1 \rangle$, doublet $|2 \...

 
 
4 hours later…
5:23 PM
0
Q: Quantifying location and volume of "lone pairs" for VSEPR

Geoff HutchisonOf course molecular shape and the VSEPR model come up frequently. As discussed previously in a valence bond picture like VSEPR, the lone pair electrons are closer to the atom than bonding pairs, and "fatter." I can think of a few ways of quantifying this, but I'm trying to add more data when disc...

 

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