[gmx-users] Concerns with g_wham

[Justin A. Lemkul]

Jennifer Casey wrote:
> Hello again,
> 
> As you mentioned, it makes sense that the starting umbrella potential a 
> in the equation U = (1/2)K(x-a)^2 should be given in the .tpr file.  I 
> have looked over the manual and online though, and I still cannot see 
> what portion of the pull code allows me to define the a.  It seems that 
> maybe GROMACS just takes the starting distance between the two atoms, 
> and centers the umbrella potential around that distance?  For instance, 
> my starting configuration starts with the reference group and pull group 
> 0.28 nm away.  I have turned on the pull code in the .tpr file in order 
> to do an umbrella sample and it looks like this:
> 
> pull = umbrella
> pull_geometry = distance
> pull_dim = Y Y Y
> pull_start = yes
> pull_ngroups = 1
> pull_group0 = Na+
> pull_group1 = I-
> pull_rate1 = 0.00
> pull_k1 = 5000
> 
> I don't see how any of these designate where the bottom of the umbrella 
> potential well lies (except for maybe pull_start - perhaps setting it to 
> yes puts centers the umbrella potential on the COM of the system).  So 
> instead, maybe GROMACS realizes that Na+ and I- start 0.28 nm away, and 
> uses this value as the center of the umbrella potential. 
> 
> Is this the case?  Or do one of these pull code designations dictate a?
> 

You've got it right.  The parameter pull_start dictates whether or not the 
starting distance is added to the value of pull_init1.  The default for 
pull_init1 is zero, so setting "pull_start = yes" tells grompp (and then mdrun) 
to "add the COM distance of the starting conformation to pull_init" (per the 
manual).  So the position of the umbrella is 0.28 (pull_start) + 0 (pull_init1) 
= 0.28 nm, in your case.

-Justin

> Thanks,
> Jennifer
> 
> On Fri, Apr 16, 2010 at 4:20 AM, Jochen Hub <jochen at xray.bmc.uu.se 
> <mailto:jochen at xray.bmc.uu.se>> wrote:
> 
>     Jennifer Casey wrote:
> 
>         Hello,
> 
>         I have been using g_wham, but I have a few questions that I
>         can't find answers to online.  When using WHAM, one does not
>         need the forces between the pull groups to calculate the PMF,
>         yet g_wham won't run without it.  Is there a reason for this?
> 
>     Hi Jennifer!
> 
>     As pointed out by Chris, you can use provide the pull positions
>     (g_wham -ix) OR the pull forces with -if. When giving the pullf
>     files, g_wham simply computes the pull positions from the forces and
>     calculates the histograms etc...
> 
> 
> 
>         Also, when using the pull code, I am allowed to define the
>         spring constant K for umbrella sampling, but I do not designate
>         where the umbrella potential is centered.  How does gromacs
>         determine this?
> 
>     Umbrella positions and force constants (and pull geometry) are taken
>     from the tpr files. That's why they must be provided to g_wham.
> 
> 
>         I am interested as I would like to create a PMF using umbrella
>         integration (from code I will write myself) rather than use
>         WHAM.  To do this and still use the umbrella sampling runs used
>         with GROMACS, I need to know where my umbrella potentials are
>         centered.
> 
>     If you want to integrate the mean forces, I would not use
>     pull=umbrella but pull=constraint. You should get the same PMF
>     compared to umbrella sampling and using g_wham.
> 
>     Please let me know if g_wham makes any trouble.
> 
>     Cheers,
> 
>     Jochen
> 
> 
>         Thank you,
>         Jennifer
> 
> 
> 
>     -- 
>     ---------------------------------------------------
>     Dr. Jochen Hub
>     Molecular Biophysics group
>     Dept. of Cell & Molecular Biology
>     Uppsala University. Box 596, 75124 Uppsala, Sweden.
>     Phone: +46-18-4714451 Fax: +46-18-511755
>     ---------------------------------------------------
> 
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at 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-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> 

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

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

========================================