Thanks for this! That makes it challenging with a system with more nanotubes then... so I will start with two. Have you ever tried to apply umbrella sampling to caluclate the PMF? Do you think it is the best way? I just want to define the equilibrium distance between two nanotube surfaces... And also if you use it which options in mdp would you recommend: pull-geometry: distance of cylinder? pull: umbrella?
I have some polypeptides attached to my both nanotubes, would the specify the index groups as nanotubes only or both nanotube+polypeptide (pull-group0 and pull-group1)? Thanks a lot, Steven On Mon, Feb 17, 2014 at 1:47 PM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > Not sure that I got your question correctly... > > The atom indices, which you supply to umbrella code, can be defined as > you like, without being bound to the molecules they belong to in the > topology files. Therefore, if you need to restraint certain number of > atoms in a system, just enumerate them within the same index group and > supply the group name to the umbrella code. > > Of course, if your aim is to compute free energies, all the involved > subsystems should be of the same composition. > > > Dr. Vitaly V. Chaban > > > > On Mon, Feb 17, 2014 at 9:38 AM, Steven Neumann <s.neuman...@gmail.com> > wrote: > > Dear Gmx Users, > > > > I am trying to setup the system of nanotubes with attached polypeptides. > I > > wish to define the equlibrium distance (PMF minima) between them. However > > in my system, I will have 6 of them in which one is in its quarter in the > > rectangular each box edge copied across pbc. It is the only one way I can > > do this as 3 nanotubes form a isosceles triangle. However if I will > change > > the distance between them, I need to change the box size. Is that > possible > > to use in Umrella Sampling with the box which difer in number of atoms > and > > box size? > > > > Or would you rather run first 1) run just 2 nanotubes - one with position > > restraints and one with harmonic potential, evaluate PMF using umbrella > > sampling (or sth else?) at different distances and then apply it with a > > second system 2) made of more of nanotubes to with the distance defined > from > > step 1)? > > > > Please, advise > > > > Steven > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.