Re: [gmx-users] Re: Re: Re: Re: umbrella potential

[Justin A. Lemkul]

Stefan Hoorman wrote:

Ok Justin, here are both profile and histogram files. Please let me know 
if you can't get access or something like this. I have never used this 
protobucket before.
"http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/profile.jpg";
"http://i784.photobucket.com/albums/yy123/stefhoor/wham_stefhoor/histogram.jpg";

The histogram shows only one peak, indicating only one window, just beyond 1.0 
nm of COM separation.  Is this an error in creating the plot, or is this really 
the result?  Like I've said before, you should have many windows, with 
overlapping distributions in order to correctly extract PMF using WHAM.

And here are my pull code stuff that is inside my mdp files. The first 
one (Pull Code 1) is the one I used to separate the structures, and the 
following (Pull Code 2) is the one used to simulate each window.

I hadn't noticed this before, and I don't know if it's meaningful, but it's 
worth looking into.  You're pulling in two dimensions.  I'm not sure the status 
of the WHAM implementation in g_wham, but it is more common in the literature to 
extract one-dimensional PMF, and this is the most commonly-used method.  I would 
suggest orienting your system such that you are pulling directly along a single 
axis, and running things again.

-Justin

; Pull Code 1
pull  =  umbrella
pull_geometry  =  distance
pull_dim  =  Y Y N
pull_nstxout  =  10
pull_nstfout  =  1
pull_ngroups  =  1
pull_group0  = Protein
pull_group1 = SLC
pull_vec1  =  1 1 0
pull_init1  =  0
pull_rate1  =  0.001
pull_k1  =  2000
pull_constr_tol  =  1e-06
pull_pbcatom0  =  0
pull_pbcatom1  =  0

; Pull Code 2
pull  =  umbrella
pull_start  =  yes
pull_geometry  =  distance
pull_dim  =  Y Y N
pull_nstxout  =  10
pull_nstfout  =  1
pull_ngroups  =  1
pull_group0  = Protein
pull_group1 = SLC
pull_vec1  =  1 1 0
pull_init1  =  0
pull_rate1  =  0
pull_k1  =  2000
pull_constr_tol  =  1e-06
pull_pbcatom0  =  0
pull_pbcatom1  =  0

The rest of my mdp stuff is pretty standard so, to save space I didn't 
post it, but if you think it is necessary I would be glad to post it as 
well. Sorry about the distance, I inverted the 2.41 (wrote 2.14). My 
separation is from starting position (close to 1nm) till 2.5. But since 
the structures always move a little in the beginning of each window, I 
guess the final maximum distance is 2.41.


------------------------------------------------------------------------

_______________________________________________
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/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/mailing_lists/users.php

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
_______________________________________________
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/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/mailing_lists/users.php