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

[Berk Hess]

Jochen Hub wrote:
> 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"?
>
In this case, I guess they should give the same results.
>> 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?

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