[gmx-users] umbrella sampling, deshuffling and version 3.3
piccinini.enrico at unimore.it
Fri Mar 10 17:28:33 CET 2006
I am using the recently released version 3.3 for my umbrella sampling runs.
I have noticed something strange in my .pdo files, which seems
conflicting with trajectory files.
This is my umbrella sampling configuration ppa file:
verbose = yes
runtype = umbrella
group_1 = K2
reference_group = REFaC
reftype = com
pulldim = N N Y
k1 = 8368.0 ;kJ mol^-1 nm^-2
pos1 = 0.006 -0.12792 2.06367
and pos1 values have been calculated trough g_traj
My .pdo files reads as follows:
# UMBRELLA 3.0
# Component selection: 0 0 1
# nSkip 1
# Ref. Group 'REFaC'
# Nr. of pull groups 1
# Group 1 'K2' Umb. Pos. 2.063670 Umb. Cons. 8368.000000
First value is known not to be zero because this is the second step
after the equilibration run. However value -0.065 means that the pulled
group is 1.998 nm above my reference group. If I check the trajectory
for the same time with g_traj i get 3.08 between pulled and reference
groups. All the other times show similar behaviour.
My results after g_wham do not seen reasonable.
I am wondering if something may got wrong due to the shuffling procedure
or something else is involved (here including my faults, eventually).
More information about the gromacs.org_gmx-users