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
[email protected] http://xray.bmc.uu.se/~michiel/
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