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Questions related to Molecular Dynamics Simulation
I selected Md_0_10.gro file and then md_0_10.xtc file then I got something weird like this in the video in vmd, can someone pls suggest what's wrong in this step?
29 August 2023 3,434 4 View
Actually, I followed some papers to calculate pKa value by using gaussian.. I need to all equations that related for this calculation Thank you so much
17 August 2023 2,440 2 View
I know that gromacs uses cuda cores of Nvidia GPUs to run. But Nvidia GPUs are excessively priced and not future proof at all. But on the other hand inelt arc GPUs (let's conside the a770) offer...
17 August 2023 2,050 2 View
hi I wanted to calculate Life-Time H-Bond I wanted to calculate the H-Bond Life-Time like this table in this article I kindly beseech your counsel and guidance in navigating this endeavor.
14 August 2023 8,175 1 View
What is quantum space, and what is quantum time? This is, in fact, the problem we call quantum gravity. We learn that there is a limit to the divisibility of space. Below a certain scale,...
14 August 2023 7,182 6 View
I have a collection (around 500) of peptide 3D structures (PDB file each 10 residues long and for a given sequence). I need to cluster it based on RMSD values among them. Is there any Python...
09 August 2023 6,205 2 View
Hello everyone, I want to creat a swirl at the exit of a conduit. I am using Ansys Fluent. The idea is to define a boundary condition (BC) at the exit of the conduit. I don't know how to set...
09 August 2023 2,629 2 View
I have seen in many studies, oxygen is used as the plasma gas source to produce ozone in the plasma chamber. But my first question is, are there any advantages if ozone is directly used as the...
04 August 2023 9,084 2 View
I conducted a 100ns simulation of my docked complex, obtaining a maximum RMSD of 4.2 Angstroms and an average of 3.1 Angstroms. Can someone help me how can I justify this high RMSD? I have...
31 July 2023 4,336 13 View
Dear fellow researchers, does anyone know how the large Protein (469 kD) DNA PKcs gets transported into the nucleues ? I know that it exists in the nucleus "in abundance" and most of its function...
31 July 2023 9,649 1 View
Hello everyone, I am using DREIDING force field to run a LAMMPS simulation for a polymeric system. I have created the structure of my system in Materials Studio and ran Dmol3 module to get...
28 July 2023 9,625 0 View
I had made a simulation box, and then after made two plates. During equilibration the atoms moves around the 'Z' axis of the simulation box. As in zhi i had taken 10. region allbox block -30 30 0...
24 July 2023 882 3 View
Please get in touch if you are willing to cooperate on a research paper with some computations on Thero-Calc. You must have a license to use the Thero-Calc software. My...
21 July 2023 1,925 3 View
How can I run a single-point TDDFT for 20 excitations? what is the command line should be in gaussian? Then I want generate NTOs from that, How can I do?
21 July 2023 5,230 3 View
I have performed GROMACS , For 1ns, 10 ns and 100ns I got proper RMSD, RMSF, RG but hydrogen bond for 100ns is not clear , 1ns and 10ns its totally fine In Xmgrace the graph is blank , The VMD...
20 July 2023 8,718 5 View
First did the NVT equilibration using below mdp file: title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog...
14 July 2023 6,755 0 View
Or if someone could provide links. Thanks!
14 July 2023 833 1 View
Hello all. My question goes back to the use of representative volume elements for modeling structures and boundary conditions needed to solve RVE in a finite element model. Assume that there is a...
13 July 2023 4,826 5 View
This question deserves to be posed and clarified. It is at this price that we will be able to consider an improvement involving analyses including new concepts. The answer to this question is...
12 July 2023 8,991 1 View
Hi everyone, Do you have any idea how we can use NPH ensemble in Gromacs? Do we need to completely delete temperature coupling options and use Parrinello-Rahman as the barostat(or maybe...
10 July 2023 8,705 3 View
gmx_mmpbsa, error,
07 July 2023 8,405 2 View
is thair any one have experience with polymer builder to generate polymers chains from monomers hetero and copolymers I need help please
05 July 2023 5,805 1 View
I have been using PRODRG for small molecules topology for years, but now I can't access it, I have emailed its developers but couldn't get any response. I want to use Gromacs forcefield, so I have...
03 July 2023 3,325 3 View
I have the text of a biomedical document and I have extracted the biomedical terms, now I want to create a connected graph that connects all the terms, I am using the Unified Medical Language...
03 July 2023 4,204 4 View