[gmx-users] g_wham problem with negative COM differences

Anni Kauko anni.kauko at gmail.com
Wed Apr 11 12:53:40 CEST 2012


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

First datalines from pullx files:
(sorry for strange file names...)

0.0000  6.26031 2.27369

0.0000  6.09702 0.0233141

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

I would appreciate help very much.


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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