[gmx-users] On the box type

Dear all, I am planing to do pulling on a bundle of elongated proteins. I compared two box types - triclinic and dodecahedron. The volume and total number of atoms (protein+solvent), following the editconf and genbox commands, were 522.06 nm3 and 47921 for triclinic box and 2444.19 nm3 and 24 f

Re: [gmx-users] On the box type

problems. Correct me if I am wrong or don't understand it right. regards, akcyrus On Sun, Jul 7, 2013 at 12:00 PM, Tsjerk Wassenaar wrote: > Hi Cyrus, > > In a rectangular box (which is a specific case of a triclinic box) your > molecule can't rotate freely without significant cha

Re: [gmx-users] On the box type

was position restrained as that did not allow it to rotate. regards, cyrus On Sun, Jul 7, 2013 at 4:45 PM, Mark Abraham wrote: > On Sun, Jul 7, 2013 at 4:15 PM, akcyrus wrote: > > Dear all and Tsjerk Wassenar, > > I could not grasp how a rectangular box will be a problem. Le