[gmx-users] g_wham problem with negative COM differences

[Justin A. Lemkul]

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

-- 
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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

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