[gmx-users] question about g_sgangle

Hi, When i used g_sgangle, i specified 2 index groups of 3 atoms each and gave the -oa flag to get the angle between them. I got two columns of output (besides the time index) - one with much larger values on the right (they look reasonable) and one with much smaller values on the left. what is th

[gmx-users] Re: question about g_sgangle

nevermind its just the cosine On Wed, May 4, 2011 at 3:36 PM, jeremy adler wrote: > Hi, > > When i used g_sgangle, i specified 2 index groups of 3 atoms each and gave > the -oa flag to get the angle between them. I got two columns of output > (besides the time index) - one w

[gmx-users] using tcl to scipt gromacs

I like to use tcl as my scripting language and after much pain and tribulation i have figured out how to get it to call gromacs without raising an error. Use exec -ignorestderr g_yourfavoritegromacsfunction. Note this will only work with versions of tcl 8.5 and later so if you use and older version

[gmx-users] issue with newest version of martini model

I am getting ab error with the newest version of the martini model in which seq2itp, atom2cg generate structures with a topology mismatch if there are any alanines in the structure 9. mutating out the alanines seems to resolve the problem? are there any bug fixes out there? thanks jeremy -- gmx-