[gmx-users] PMF a straight line with PULL

[Michiel van Lun]

Dear all,

I have used the PULL code in gmx 4 to pull a compound out of a protein 
complex. I would like to obtain a free energy profile.
A series of pull runs were performed. Pulling works fine as seen from 
trajectory and pullx.xvg. After using g_wham the profile.xvg graph 
displays a surprising straight line. The histogram looks ok though. Can 
anyone tell me what I am missing?

The commands:
mdrun -dd 12 8 1 -npme 32 -v -o -x -e -c -compact -s topol.tpr -pf -px
g_wham -if if.dat -it it.dat

The profile.xvg file:
@    title "Umbrella potential"
@    xaxis  label "z"
@    yaxis  label "E (kJ mol\S-1\N)"
@TYPE xy
-1.488717e+00   nan
-1.438949e+00   nan
-1.389181e+00   nan
-1.339413e+00   nan
-1.289645e+00   nan
-1.239877e+00   nan
-1.190109e+00   nan
-1.140341e+00   nan
-1.090573e+00   nan
-1.040805e+00   nan
-9.910373e-01   nan
(.....)
7.967203e+00    inf
8.016971e+00    inf
8.066739e+00    inf
8.116507e+00    inf
8.166275e+00    inf
8.216043e+00    inf
8.265811e+00    inf
8.315579e+00    inf
8.365347e+00    inf
8.415115e+00    inf

The pull options:
; PULL
pull            = umbrella
pull_geometry   = distance      ;distance, direction, cylinder, position
pull_dim        = Y Y Y
;pull_r1        = 1             ; (1) [nm]
;pull_r0        = 1.5           ; (1) [nm]
;pull_constr_tol= 1e-6          ; (1e-6)
pull_start      = yes ; that means that is is starting exactly where the 
COM is
pull_nstxout    = 10            ; (10)
pull_nstfout    = 1             ; (1)
pull_ngroups    = 1             ; (1)
pull_group0     = system        ; name of the reference index group, not 
the nr
;pull_weights0  =
;pull_pbcatom0  =               ; (0)
pull_group1     = CO2           ; name of the group to pull on
;pull_weights1  =
;pull_pbcatom1  =               ; (0)
pull_vec1       = 0 0 0         ; (0.0 0.0 0.0)
pull_init1      = 5     ; (0.0) / (0.0 0.0 0.0) [nm]: x&y don't matter!
pull_rate1      = 0.01          ; (0) [nm/ps]
pull_k1         = 100           ; (0) [kJ mol-1 nm-2] / [kJ mol-1 nm-1]
;pull_kB1       = 0             ; (pull_k1) [kJ mol-1 nm-2] / [kJ mol-1 
nm-1]

A small addition to the pull options: this is supposed to give a radial 
(rather than vector) displacement. Using pull_vec1= 0 0 1 will give same 
result in PMF.

Any help is appreciated,

-- 
Michiel van Lun, MSc
Swedish University of Agricultural Sciences
Uppsala Biomedical Centre
Husargatan 3, Box 590
SE-75124 Uppsala, Sweden
tel: +46 18 471 4537 fax: +46 18 511 755
michiel at xray.bmc.uu.se    http://xray.bmc.uu.se/~michiel/
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