Hi,
I have a system with 30nm Diameter DPPC vesicle in CG Martini force field, and I want to calculate the stress profile of it. Is there any tool/plugin to do that?
Hello everyone! I am using Plumed-2.2.2 patched with Gromacs-5.1.2 (GPU version) to run a WT-MetaD for a peptide-bilayer system. The three CVs I use are: (1.) bilayer-peptide distance in...
03 April 2018 9,451 1 View
I have a bilayer-vesicle system in CG Martini model. I want to pull the vesicle towards the bilayer in order to fuse them together. I want to put the bilayer as reference without putting any...
11 December 2016 7,097 4 View
Hello, I have a coarse grained (Martini) system containing a DPPC bilayer and DPPC spherical vesicle, and I want to study surface tension induced fusion between the two. I want to apply constant...
10 November 2016 5,353 1 View
I am trying to run an atomistic MD simulation (CHARMM36 FF) for a lipid-peptide assembly, where the peptide is kept on the top of an atomistic bilayer. The peptide is linked to one of the lipid...
08 September 2016 953 7 View
I want to simulate a vesicle system with DLPC lipids in Martini CG force field. I generate the initial structure from CHARMM-GUI as well as from Packmol. But after energy minimization, I run into...
07 August 2016 7,741 4 View
Hi, I am trying to do a md run on a CG system of solvated lipid vesicle using Gromacs 5.1.2 and Martini force field. I am getting this particular error: ---------- Program gmx mdrun, VERSION...
07 August 2016 7,066 1 View
I am trying to restart a Replica Exchange simulation (50 replicas on 100 cores) and the run is not giving any output. The simulation seems to be started because the .log files got updated (just...
01 February 2016 7,390 3 View
Hi, I patched gromacs 5.0.2 with plumed 2.2.1 (version meant for gromacs 5.0.4) and I am trying to run the belfast tutorial. While starting the simulation and running the mdrun -plumed, I get this...
01 February 2016 5,390 2 View
I have a system with lipid-linker-peptide. I have the force field parameters for the lipid as well as for the peptide, but not for the linker (which is a molecular fragment prepared in the lab to...
01 February 2016 8,446 3 View
I am having a system with 450 Protein atoms and ~9000 water atoms. When I am trying to do the energy minimization step, it gives me hundreds of trajectory files (all .pdb with names like...
31 December 2015 2,246 4 View
Could you recommend some articles on Urban Transportation System optimization and Innovation?
13 August 2024 2,595 3 View
We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...
08 August 2024 4,842 0 View
Hi, I'm currently working on a project where I need to plot the atom-projected band structure using GPAW. I've been able to calculate the band structure for my material, but I'm having trouble...
07 August 2024 269 3 View
I am interested to know the behavior of dyes toward light. Specifically, Blue dyes re-emit the spectrum, especially from the green zone (known as principal in LED lamps, and blue dyes are known...
05 August 2024 3,290 1 View
What is the role of oxidative stress in toxin-induced carcinogenesis? I am currently researching the impact of environmental toxins on children's health and would greatly appreciate insights from...
02 August 2024 3,174 1 View
All plants are green but some of these plants becomes yellow. I did not found any reason. Please help me to find out the real problem.
01 August 2024 589 4 View
Hello everyone What is your opinion about the introduction of an expert decision support system in which the rules are extracted from existing data without human intervention, instead of being...
31 July 2024 5,785 4 View
After a lot of feature engineering for click-through rate modeling, it feels like it's basically the end of iteration? I mean, it's not cost-effective to keep doing it?
29 July 2024 4,955 0 View
Our department has recently acquired an HPC (High-Performance Computing) system, and I'm thrilled to take my molecular dynamics calculations to the next level using Desmond. I used to run my...
28 July 2024 6,553 1 View
i compare between the antioxidant and oxidative stress level between negative control rats (saline) and CCL4 intoxicated rats. i found the level of GSH and TAC is more in toxic group than normal....
26 July 2024 1,887 0 View