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

[Jochen Hub]

Berk Hess wrote:
> 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.
>   
Hm, actually I have used "position" quite often it it gave the same 
result compared to using position restraints as umbrella potentials, so 
it seems fine. Is it possible that using position with "pull_dim=N N Y" 
is the same as direction with "pull_vec1=0 0 1"?

> 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.

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
>>>>>
>>>>>
>>>>>       
>>>>>           
>>>>     
>>>>         
>>>   
>>>       
>>     
>
>   


-- 
---------------------------------------------------
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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