Open keisuke-yanagisawa opened 5 years ago
I'd be happy to accept any contribution that adds this, but it is beyond my experience to do it quickly.
The only virtual site geometries that I've supported are the ones supported by Amber and used in common all-atom force fields -- specifically those used by TIP[45]P water models.
Dear swails,
Thank you for your comments. According to the Gromacs documentation, three types of virtual_sitesn can be defined:
MARTINI uses COM and I haven't seen COW yet, thus I believe the priority order is COM > COG >>>> COW
if you kindly will implement it.
Probably below documentation pages are helpful: Types of virtual_sitesn: http://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#tab-topfile2 Notation of virtual_sitesn: http://manual.gromacs.org/current/reference-manual/topologies/particle-type.html?highlight=virtual_site
Hi everyone,
Now I'm searching a way to generate gromacs topology file with virtual_sitesn direction (extra point at center-of-mass of selected atoms).
I have written below code:
In the case 1, the code can output topology file but res ZZZ does not have VIR atom. On the other hand, case 2 raised an AttributeError:
I realized the error says I have to determine the type of frame, but I could not find corresponding frame type to virtual_sitesn in Gromacs.
virtual_sitesn is used by some known tools (such as MARTINI), thus I believe it is possibly helpful enhancement while there may be difficult point to implement. I would be glad if admins discuss it, and furthermore, it implements.