Swapnil Wagle

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Questions related from Swapnil Wagle

Why do I get this segmentation fault in WT-MetaDynamics?

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 9,409 1 View

Gromacs: How to set bilayer as reference in umbrella sampling?

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 7,063 4 View

Gromacs MD simulation: What is the relation between surface tension and lateral pressure in lipid bilayer?

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 5,313 1 View

How to calculate stress profile of a Vesicle?

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 6,377 0 View

Why does the structure break during MD simulation, and the simulation crashes?

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 908 7 View

Martini CG force field: Is it possible to simulate DLPC vesicles?

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 7,703 4 View

Gormacs: Why am I getting this error?

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 7,032 1 View

Gromos 53a6 force field: How to calculate partial atomic charges for a molecular fragment?

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

Internal PLUMED error: Why am I getting this error while running PLUMED 2.2.1 patched with gromacs 5.0.2?

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 5,355 2 View

Gromacs: Error in restarting Replica Exchange simulation. How to interpret this error message?

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 7,342 3 View

Why GROMACS is generating so many output trajectory files?

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 2,208 4 View

How to split an MD trajectory file (in .PDB format) to smaller trajectory files (also in .PDB format)?

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 5,886 2 View