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

[Jochen Hub]

Berk Hess wrote:
> Hi,
>   
Hi Bert,

thanks for the quick reply.

> Why are you using position and not distance (both should work though)?
>   
Because I need to distinguish between above and below the membrane, 
whereas "distance" does not. But with "distance" we get the same wrong 
output, I just checked.
Pull group  natoms  pbc atom  distance at start     reference at t=0
       0      5896      2948
       1         4      5898   2.326                 2.920             

Here, distance and reference should be close to each other (according to 
g_traj -com).

> Do your pull group and reference group have atoms in common?
>   
No, no common atoms.

> BTW 4.0.7 is the version to use for pulling, but I think there are no fixes
> related to your situation.
>   
With 407 we get the same output from grompp.

Cheers,

Jochen


> Berk
>
> Jochen Hub wrote:
>   
>> 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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