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 9,194 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 6,946 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 5,229 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 805 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 7,548 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 6,836 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 7,192 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 5,216 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 8,324 3 View
I want to run an analysis on the molecular trajectory file of my system (protein with 400 atoms). When I run the analysis script on the PDB file, it stops with an error 'Aborted (core dumped)' The...
31 December 2015 5,745 2 View
I'm targeting to deploy a mesh network and manually configure MANET routing protocols. I'm preparing scenarios, architectures, and hard devices needed to do that. Are there some step-by-step...
03 March 2021 1,931 5 View
I have dataset which shows the length of power lines. I need to classify the lines based on the line length. Is there a rule to classify the High voltage (HV) and low voltage (LV) lines based on...
03 March 2021 4,116 4 View
The range of forms and sizes of cavities in rock is very big. Is there a classification scheme for rock cavities regarding their size and shape?
02 March 2021 4,511 3 View
Is there a powerful system for the security of the systems distributed on IoT systems?
02 March 2021 3,858 10 View
I want to do a parameter study of a aixsymmetric cylinder in Abaqus. I want to create several jobs where I get the stresses for 3 different points in my model. These points are defined. I wrote a...
01 March 2021 10,078 1 View
Hi. I am doing non linear FE analysis using a new material beam under flexural 2 point loading using ANSYS. I have defined a bilinear material model. The solution has converged. In results I am...
01 March 2021 9,911 3 View
Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...
01 March 2021 8,747 4 View
Which is suitable for use with Python? MySQL or SQL Server? What is your suggestion?
01 March 2021 3,422 3 View
Hello, I spin-cast two different polymers onto wafers and measure their height as a function of initial concentration. For polymer A, I have the weight-average molecular weight (Mw) as well as...
28 February 2021 7,882 2 View
I like to do project in laser measurement system. My objective is to eliminate or reduce the cosine error, abbe error in Laser measurement system. I have Rhenishaw XL80 system. Please tell the...
28 February 2021 4,890 3 View