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

[Jochen Hub]

>>> Can you try if that also gives problems?
>>>
>>>   
>>>       
>> I have tried, one gets with
>> pull_geometry            = direction
>> pull_dim                 = N N Y
>> pull_vec1                = 0.0 0.0 1.0
>> pull_init1               = -2.91975
>>
>> Pull group  natoms  pbc atom  distance at start     reference at t=0
>>       0      5896      2948
>>       1         4      5898  -2.326                -2.920            
>> which is again wrong (and the negative to the "distance" output, as
>> expected). The correct distance in z-direction is (this time from
>> g_dist) -2.9742942, not -2.326.
>>
>>     
> Ah, couldn't the problem simply be a pbc issue?
> What is your z box size?
> And it your pull pbc reference atom set properly?
>   
Ah, good point. The box in z-direction is however definitely large 
enough. None of the atoms of the reference group atoms is outside the 
box in z-direction. I have a bilayer well in the middle of the box in 
z-direction.

However, the pbc atom is sometimes out of the box in x-direction since 
the the initial structure contains non-broken lipids which sometimes 
point out of the box (in the x-y plance). This is definitely the 
problem. When using a pbc_atom in the middle of the bilayer everything 
goes fine. Using a pdb with atoms inside the box does however not help, 
apparently the pull code used non-broken molecule coordinates.

So we found the issue (thanks for that!), but is that the expected 
behavior? I would expect that, if I only pull in z-direction, a pbc_atom 
out of the box in x-y should not affect the reference position. Or am I 
wrong here?

Thanks a lot Berk,

Jochen



> Berk
>
>   
>> Jochen
>>
>>
>>
>>     
>>> 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
>>>>>>>
>>>>>>>
>>>>>>>                 
>>>>>>>               
>>>>>>             
>>>>>>             
>>>>>         
>>>>>           
>>>>     
>>>>         
>>>   
>>>       
>>     
>
>   


-- 
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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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