[gmx-users] Cylinder Pulling output file pullx.xvg wron

[chris.neale at utoronto.ca]

That part of the pull code has a different printf statement in version  
4.5.3. Can you test 4.0.7 output vs. 4.5.3 output and see if 4.5.3 is  
correct? You could simple use nsteps=0 genvel=no and load a .gro with  
no velocities in your mdrun.

Chris.

-- original message --

I am trying cylinder pulling as an option of umbrella sampling using gromacs
4.0.7. Things seem to work but I noticed that in the output file pullx.xvg,
the referece group's postion is always 0. I don't think it is right. When I
use position pulling, the reference position is never 0.

Thanks for you help.
Kun

Below is my .mdp file
pull                    = umbrella
pull_geometry           = cylinder
pull_r1                 = 1.0
Pull_r0                 = 1.0
pull_dim                = N N Y
pull_start              = yes
pull_init1              = 0.0
pull_ngroups            = 1
pull_group0             = group0
pull_group1             = group1
pull_rate1              = 0.01
pull_vec1               = 0.0 0.0 -1.0
pull_k1                 = 3000      ; kJ mol^-1 nm^-2
pull_nstxout            = 1000
pull_nstfout            = 1000

Here is the output:

@    title "Pull COM"
@    xaxis  label "Time (ps)"
@    yaxis  label "Position (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "0 Z"
@ s1 legend "1 dZ"
0.0000  0   5.69818
2.0000  0   5.67685
4.0000  0   5.68564
6.0000  0   5.65461
8.0000  0   5.63482
10.0000 0   5.61658
12.0000 0   5.61679
14.0000 0   5.54434
16.0000 0   5.55352
18.0000 0   5.4964
-------------- next part -------------