[gmx-users] umbrella sampling with distances larger than half box size

[lloyd riggs]

I would wait for others to answere but,

a) you might try orienting your circular DNA in a visual program first and then use say just pull nny or something just as it makes it easier to see output and makes restraints nicer in output,

b) the pull k1 might be larger for an effect on macromolecules, ie in some protein work its around 2000-3000 but I have also seen some with 1000, however these are 300-1000 aminos or larger proteins so do not know how it would translate to DNA

c) Just increase your deminsions in 1 direction from the pull defined in a) or your origional vector

Aside,  Like I said Im a novice so others might have more usefull information.

Stephan Watkins

-------- Original-Nachricht --------
> Datum: Sun, 24 Jun 2012 13:09:34 +0200
> Von: anaome at fundp.ac.be
> An: gmx-users at gromacs.org
> Betreff: [gmx-users] umbrella sampling with distances larger than half box	size

> Dear Users,
> 
> I am performing umbrella sampling simulations of the ring closure of  
> DNA minicircles. The problem with pull_geometry=distance is that the  
> end-to-end distance used as general coordinate becomes at some point  
> larger than half the box size. The distance to the closest image is  
> used in the histogram generation and WHAM procedure what is of course  
> wrong. To avoid this problem I tried pull_geometry=direction_periodic  
> with pull_vec1 taken as the vector between both ends of the DNA  
> fragment and one end frozen but this set-up does not seem to work  
> properly. Does anyone have a solution? Is there a possibility to  
> implement a pull_geometry=distance_periodic in a next version of  
> gromacs?
> 
> Thank you for helping!
> 
> Below are the relevant options used for umbrella sampling:
> pull                     = umbrella
> pull_geometry            = distance
> pull_dim                 = Y Y Y
> pull_start               = yes
> pull_ngroups             = 1
> pull_group0              = start
> pull_group1              = end
> pull_k1                  = 100
> 
> 
> pull                     = umbrella
> pull_geometry            = direction_periodic
> pull_dim                 = Y Y Y
> pull_start               = yes
> pull_ngroups             = 1
> pull_group0              = start
> pull_group1              = end
> pull_vec1=-0.4160005.3 -0.2650005.3 -2.4920005.3
> pull_k1                  = 100
> freezegrps               = start
> freezedim                = Y Y Y
> 
> 
> 
> -- 
> Aymeric Naômé
> Ph. D. Student
> UCPTS Division
> University of Namur
> 61 Rue de Bruxelles
> 5000 Namur
> BELGIUM
> 
> 
> -- 
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone!                                  
Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a