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

[Berk Hess]

Jochen Hub wrote:
> 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).
Sorry, direction is what you probably want.
Can you try if that also gives problems?

Berk
>
>> 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
>>>>
>>>>
>>>>       
>>>     
>>
>>   
>
>