[gmx-users] g_wham problem with negative COM differences
akauko at sbc.su.se
Fri Apr 13 08:30:47 CEST 2012
> 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.
> you can reconstruct the PMF by separately analyzing the positive restraint
> distances and negative restraint distances (note here that "distance"
> refers to a vector quantity, and thus it can have a sign), or otherwise
> new .tpr files using "position" geometry, though I don't know if g_wham
> accept them or not.
> 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
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.
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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users