Dear Gromacs Users! By that moments I've completed 2 sets of simulation in high temperature
1- With applied posres on the backbone atoms ( fc= 200 ). The result was- that the posres prevented motion of the helixes as the rigid bodies so I've not noticed any conformation sampling. Question : Could I observe some conformation sampling on that trajectory by means of some external tricks ? E.g extracting of the eigenvectors via PCA? 2 With applied network of disres applied on backbone atoms of the helix elements of my protein within Rc=1nm. As the result of that simulation I've observed distortion of my protein wich resulted in some kind of shrinking of the helix elements. Question : How I could specify that disres more correctly ? If I've observed some kind of shrinking of my protein does it means that Rc was chosen incorectly or should I define disres in anothe manner ? ( I'have not quite understand what exatly is the R_fract and in what situation it could be useful ). James
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
