[gmx-users] g_wham problem with negative COM differences

[Anni Kauko]

> Date: Wed, 11 Apr 2012 08:38:05 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] g_wham problem with negative COM differences
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4F857B2D.3050100 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Anni Kauko wrote:
> > Hi!
> >
> > I try to perform pmf calculations for case where a peptide shifts
> > through the membrane. My COM differences should vary from 2.3 to -2.5.
> >
> > My problem is that g_wham plots negative COM difference as they would be
> > positive.  In pullx-files the COM differences are treated correctly
> > (look below). My peptide is not symmetric, so profile curves are not
> > symmetric, so loosing the sign for COM difference screws my profile
> > curve completely.
> >
> > I did not manage to find any pre-existing answers to this problem from
> > internet.
> >
> > First datalines from pullx files:
> > (sorry for strange file names...)
> >
> > pull_umbr_0.xvg:
> > 0.0000  6.26031 2.27369
> >
> > pullz_umbr_23.xvg:
> > 0.0000  6.09702 0.0233141
> >
> > pullz_umbr_50.xvg:
> > 0.0000  6.02097 -2.50088
> >
> > g_wham command:
> > g_wham -b 5000 -it tpr_files.dat  -ix pullz_files.dat -o
> > profile_test.xvg -hist histo_test.xvg  -unit kCal
> >
> > My pull code:
> >
> > pull            = umbrella
> > pull_geometry   = distance
> > pull_dim        = N N Y
> > pull_start      = yes
> > pull_ngroups    = 1
> > pull_group0     = POPC_POPS         ; reference group is bilayer
> > pull_group1     = C-alpha_&_r_92-94 ; group that is actually pulled
> > pull_init1      = 0
> > pull_rate1      = 0.0
> > pull_k1         = 1000     ; kJ mol^-1 nm^-2
> >
>
> Your problem stems from the use of "distance" geometry.  This method
> assumes the
> sign along the reaction coordinate does not change, i.e. always positive or
> always negative.  If the sign changes, this simple method fails.  You
> should be
> using something like "position" to allow for a vector to be specified.
>  Perhaps
> you can reconstruct the PMF by separately analyzing the positive restraint
> distances and negative restraint distances (note here that "distance"
> really
> refers to a vector quantity, and thus it can have a sign), or otherwise
> create
> new .tpr files using "position" geometry, though I don't know if g_wham
> will
> accept them or not.
>
> -Justin
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
Thank's!

I managed to solve my g_wham problem by doing two things:

1. New tpr-files with proper pull code for g_wham.
2. I also needed to modify signs of pullf values: If value for pullx
distance was negative, I reversed the sign of corresponding pullf value. I
did that by my own script.

The new pull code:

; Pull code

pull            = umbrella
pull_geometry   = direction
pull_vec1       = 0 0 1
pull_start      = yes
pull_ngroups    = 1
pull_group0     = POPC_POPS         ; reference group is bilayer
pull_group1     = C-alpha_&_r_92-94 ; group that is actually pulled
pull_init1      = 0
pull_rate1      = 0.0
pull_k1         = 1000     ; kJ mol^-1 nm^-2

I am little bit confuced, why I needed to tweak signes of pullf values. But
like that I got the curve that resembles two half curve made for positive
and negative pullx distances separately. That curve also makes sense from
biochemical point of view.

-Anni

PS. Thank's for your excellent tutorials. They have been indispensable help
for me to get started with gromacs!

-- 
************************************************
Anni Kauko, Ph.D.
Post Doctoral Researcher

Structural Bioinformatics Laboratory
Dept. of Biosciences, Biochemistry
Åbo Akademi University
20520 Turku, Finland
phone:  +358 (0)2 215 4006
mobile: +358 (0)50-576 8656

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