Swapnil Wagle

3 Questions 11 Answers 0 Followers

Questions related from Swapnil Wagle

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...

06 December 2016 629 3 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...

05 February 2016 7,981 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...

13 January 2016 304 3 View