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

[Berk Hess]

Hi,

Why are you using position and not distance (both should work though)?
Do your pull group and reference group have atoms in common?

BTW 4.0.7 is the version to use for pulling, but I think there are no fixes
related to your situation.

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
>>
>>
>
>