[gmx-developers] center of mass bug with pulling reference group

Jochen Hub jochen at xray.bmc.uu.se
Mon Apr 26 13:41:52 CEST 2010


we are facing strange behavior of the center of mass of the reference 
group when doing umbrella sampling. We are doing umbrella simulations in 
z-direction across a membrane lipid bilayer

pull                     = umbrella
pull_geometry    = position
pull_dim             = N N Y
pull_group0        = lipid1_lipid2 ; or lipid1 or lipid2
pull_group1        = solute
pull_weights1     =
pull_pbcatom1    = 0
pull_vec1            = 0.0 0.0 0.0
pull_init1            = 0 0 -2.91975
pull_rate1            = 0
pull_k1                = 800
pull_kB1             = 0

The membrane contains two types of molecules (lipid1 and lipid2), which 
are equally distributed over the two membrane monolayer. If we use only 
lipid1 as reference group, or only lipid2 as reference group, everything 
is fine. But as soon as we have both groups in the reference 
(pull_group0), the COM of the reference group gets obviously wrong (and 
does not agree with the result from g_traj -com). The error is visible 
from the grompp output and from the pullx file. For example, if we use

pull_group0   = lipid1  or
pull_group0   = lipid2, grompp writes
Pull group  natoms  pbc atom  distance at start     reference at t=0
       0      5200      2600
       1         4      5898   0.000  0.000 -2.976   0.000  0.000 -2.920
(distance at start and reference distance agree, in agreement with 
g_traj -com.)

where as with the merged pull_group0=lipid1_lipid2
Pull group  natoms  pbc atom  distance at start     reference at t=0
       0      5896      2948
       1         4      5898   0.000  0.000 ** -2.326 **   0.000  0.000 

We have have been extra-careful that the index file is fine and there 
seems to be no issue with the PBC in z-direction.

Is there something that I missed? Should I file a bugzilla?



Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

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