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Questions related from Swapnil Wagle
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...
04 April 2018 9,406 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...
12 December 2016 7,062 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...
11 November 2016 5,311 1 View
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?
09 September 2016 6,376 0 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...
09 September 2016 907 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...
08 August 2016 7,702 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...
08 August 2016 7,029 1 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...
02 February 2016 8,402 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...
02 February 2016 5,351 2 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...
02 February 2016 7,341 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...
01 January 2016 2,207 4 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...
01 January 2016 5,884 2 View
