LIGPLOT failed-no atom coords found
possibly this case is too difficult to plot
My system contains protein-ligand complex in water, neutralized by adding Na and Cl ions.
01 February 2019 9,081 2 View
Can 2D plot (from ListContourPlot) and 3D plot (from ListPlot3D) be combined so that the 2D plot is the bottom surface of the 3D plot? I am not able to join it using Show. I have a 2d plane...
02 March 2018 6,073 2 View
Is there any software or online server for charge calculation of organic molecules?
11 December 2016 197 3 View
I need to simulate a protein with NAD cofactor as well one other ligand. Is it possible with gromacs?
09 October 2016 1,256 4 View
Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...
03 March 2021 9,989 2 View
(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...
02 March 2021 3,309 2 View
for all the rheology researchers, my question is, how relevant is a mini slump cone (smaller than a standard 50 cent rheometer). currently based on testing, the thickness of slumped material is...
26 February 2021 3,668 1 View
during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...
22 February 2021 380 5 View
MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...
21 February 2021 9,538 3 View
Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?
20 February 2021 3,134 5 View
For example, I have this phonon dispersion(Fig. 1), and now I would like get vector of atoms which describes TA1 in P. I know v_sim can show vibrational animation of specific mode, but I do not...
20 February 2021 4,332 4 View
I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...
19 February 2021 1,236 1 View
I am trying to simulate contact angle of water on a quartz slab using LAMMPS. I have created and equilibriated the quartz slab and the water cluster separately. Now I want to create a composite...
17 February 2021 5,884 2 View
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