First of all, I want to thank the developers for their effort in implementing this and all the Martini-related tools, this work is amazing.
I am trying to use fast_forward to parametrize a set of polymers. My idea is to take advantage of all the new features of the Martini toolkit, so I built a library of pieces using Amber (e.g., Tail1, Core1, Core2, Head1). Then, I created a library of maps (e.g., Tail1.map, Core1.map, Core2.map, Head1.map). The next step is to directly go to polyply.
What I want to do is use the map library to automatically map all possible combinations of polymers. The only problem is that I have a bead that could be shared between two pieces (for example, a bead that includes some atoms at the end of Head1 and some at the start of Core1).
When using ff_map, the program creates two different beads with the same name at the connection between the two residues. I have read issue #17, which seems to be related to this problem and refers to cgsmile, but I am struggling to understand how I can use this feature. Do I have to employ cgsmiles to deal with this problem or there are others possible workaround, like in polyply where I set rules when I stack two units?
First of all, I want to thank the developers for their effort in implementing this and all the Martini-related tools, this work is amazing.
I am trying to use fast_forward to parametrize a set of polymers. My idea is to take advantage of all the new features of the Martini toolkit, so I built a library of pieces using Amber (e.g., Tail1, Core1, Core2, Head1). Then, I created a library of maps (e.g., Tail1.map, Core1.map, Core2.map, Head1.map). The next step is to directly go to polyply.
What I want to do is use the map library to automatically map all possible combinations of polymers. The only problem is that I have a bead that could be shared between two pieces (for example, a bead that includes some atoms at the end of Head1 and some at the start of Core1).
When using ff_map, the program creates two different beads with the same name at the connection between the two residues. I have read issue #17, which seems to be related to this problem and refers to cgsmile, but I am struggling to understand how I can use this feature. Do I have to employ cgsmiles to deal with this problem or there are others possible workaround, like in polyply where I set rules when I stack two units?