[gmx-users] g_wham: How to get the umbrella positions from pullf.xvg when pull-start = no?
lipingsunshine at gmail.com
Fri May 6 11:06:39 CEST 2016
I'm doing umbrella samplings using gromacs_4.6.3 after pulling the glucose
through a channel. Here is my pull code:
; Pull code
pull = umbrella
pull_geometry = direction
pull-vec1 = 0.0 0.0 -1.0
pull-dim = N N Y
pull-start = no
pull_ngroups = 1
pull_group0 = channel
pull_group1 = glucose
pull_rate1 = 0.0
pull_k1 = 1000
pull-init1 = 0.0
I chose "pull-start = no" because the resulting "umbrella positions" were
totally inversed when I used "pull-start = yes". Therefore, the positions
of each sample is around zero. From what I understood, I can calculate the
"umbrella positions" along "time" from pullf.xvg. Then add the "start
position" to each "umbrella positions" and get the .pdo files like the
# UMBRELLA 3.0
# Component selection: 0 0 1
# nSkip 1
# Ref. Group 'channel'
# Nr. of pull groups 1
# Group 1 'glucose' Umb. Pos. ??? Umb. Cons. 1000.0
The problem is how I can calculate the "umbrella positions" along "time"
from pullf.xvg??? Or is there another way to obtain the .pdo files?
Thank you very very much!
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