GROMACS version:2019.6
GROMACS modification: Yes/No
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Dear all,
I refer to GROMACS Tutorial -Umbrella Sampling written from Justin A. Lemkul (thanks a lot for the devotion of this tutorial) to simulate two parellel sheet’s pulling, namely fix one sheet and drag another sheet at z axis.
My pull code is belowed,
(first pull code)
gen_vel = no
;
pull = yes
pull-ngroups = 1
pull-group1-name = red
pull-ncoords = 1
pull-coord1-type = umbrella
pull-coord1-geometry = direction
pull-coord1-groups = 0 1
pull-coord1-rate = 0.001
pull-coord1-init = 5.51
pull-coord1-vec = 0 0 1
pull-coord1-dim = N N Y
pull-coord1-k = 400
;
freezegrps = red yellow purple gray
freezedim = Y Y N Y Y Y Y Y Y Y Y Y
(one window pull code) I modified the pull-coord1-init according to the com of the pulling sheet for each window.
gen_vel = yes
;
pull = yes
pull-ngroups = 1
pull-group1-name = red
pull-ncoords = 1
pull-coord1-type = umbrella
pull-coord1-geometry = direction
pull-coord1-groups = 0 1
pull-coord1-rate = 0.0
pull-coord1-init = 5.53492
pull-coord1-vec = 0 0 1
pull-coord1-dim = N N Y
pull-coord1-k = 400
;
freezegrps = red yellow purple gray
freezedim = Y Y N Y Y Y Y Y Y Y Y Y
After running these windows’ simulation, I got the md.tpr and pullf.xvg, which were integrated in tpr.dat and pullf.dat.
When I use the command, gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal, warning information were listed belowed.
Command line:
gmx wham -it tpr.dat -if pullf.dat -o -hist
Found 7 tpr and 7 pull force files in tpr.dat and pullf.dat, respectively
Reading 7 tpr and pullf files
Automatic determination of boundaries…
Reading file umbrella0.tpr, VERSION 2019.6 (single precision)
File umbrella0.tpr, 1 coordinates, with these options:
Geometry direction k = 400 position = 5.53492 dimensions [N N Y] (1 dimensions). Used: Yes
Pull group coordinates of 0 groups expected in pullx files.
Reference value of the coordinate not expected in pullx files.
Use option -v to see this output for all input tpr files
Reading pull force file pullf-umbrella0.xvg, expecting 2 columns:
Columns for pull coordinate 1
reaction coordinate: 1
center-of-mass of groups: 0
reference position column: No
Found 201 times in pullf-umbrella0.xvg
Reading file umbrella16.tpr, VERSION 2019.6 (single precision)
Reading file umbrella29.tpr, VERSION 2019.6 (single precision)
Reading file umbrella43.tpr, VERSION 2019.6 (single precision)
Reading file umbrella72.tpr, VERSION 2019.6 (single precision)
Reading file umbrella476.tpr, VERSION 2019.6 (single precision)
Reading file umbrella753.tpr, VERSION 2019.6 (single precision)
Determined boundaries to 100000002004087734272.000000 and -100000002004087734272.000000
Reading file umbrella0.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella0.xvg (check -b option)
Reading file umbrella16.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella16.xvg (check -b option)
Reading file umbrella29.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella29.xvg (check -b option)
Reading file umbrella43.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella43.xvg (check -b option)
Reading file umbrella72.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella72.xvg (check -b option)
Reading file umbrella476.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella476.xvg (check -b option)
Reading file umbrella753.tpr, VERSION 2019.6 (single precision)
WARNING, no data points read from file pullf-umbrella753.xvg (check -b option)
Program: gmx wham, version 2019.6
Source file: src/gromacs/gmxana/gmx_wham.cpp (line 2570)
Fatal error:
No data points were found in pullf/pullx files. Maybe you need to specify the
-b option?
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs
The part pullf.xvg were listed belowed.
Command line:
gmx mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
gmx mdrun is part of G R O M A C S:
GROup of MAchos and Cynical Suckers
@ title “Pull force”
@ xaxis label “Time (ps)”
@ yaxis label “Force (kJ/mol/nm)”
@TYPE xy
0.0000 4000
0.0500 3989.23
0.1000 3967.93
0.1500 3946.81
0.2000 3922.88
0.2500 3899.1
0.3000 3873.36
0.3500 3850.97
0.4000 3830.18
0.4500 3809.47
0.5000 3789.49
0.5500 3773.73
0.6000 3759.7
0.6500 3747.62
0.7000 3738.23
0.7500 3735.11
0.8000 3729.7
0.8500 3726.62
0.9000 3724.14
0.9500 3722.91
1.0000 3719.86
How can I solve this question? Thank you all very much.