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

[Jochen Hub]

Sorry, I forgot: We have tried with the gmx-master and with 4.05.

Jochen


Jochen Hub wrote:
> Hi,
>
> 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 
> -2.920
>                                                          ^^^^^^^^^^
>
> 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?
>
> Cheers,
>
> Jochen
>
>


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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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