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 -------------
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
