[gmx-users] ligand moving out during umbrella sampling

[abhisek Mondal]

On Thu, May 11, 2017 at 9:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/11/17 9:21 AM, abhisek Mondal wrote:
>
>> On Thu, May 11, 2017 at 11:02 AM, abhisek Mondal <abhisek.mndl at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> Thank you for the explanation. It really cleared some concepts. But I'm
>>> still having my ligand moving in this step. I have modified the code as:
>>> ; Pull code
>>> pull                    = umbrella
>>> pull_ngroups            = 1
>>> pull_group0             = Protein_chain_A
>>> pull_group1             = ACO
>>> pull_geometry           = direction ; simple distance increase
>>> pull_dim           = Y Y Y         ; not to allow ligand move along other
>>> dir
>>> pull_rate1         = 0.0
>>> pull_k1           = 1000           ; kJ mol^-1 nm^-2
>>> pull_start       = yes           ; define initial COM distance > 0
>>> pull_vec1               = 0 0 -1
>>>
>>>
> Note that with "direction" geometry, only pull_vec1 is acting.  pull_dim
> is ignored.
>
> The ligand was previously moving along x,y direction when I was using
>>> pull_dim  = N N Y. So I changed it to Y in all direction and provided 0
>>> as
>>> vector  and pull_rate1=0.0, so that it does not move much. But at the end
>>> of a 10ns run, I see that the ligand is still moving as it was earlier.
>>>
>>> It shows me:
>>  Pull group  natoms  pbc atom  distance at start     reference at t=0
>>        0      1132    936665
>>        1        59      1618  -1.555                -1.555
>> Is it ok withe negative value ? Anyway this setup is not working.
>>
>>
> Again you're trying to just apply the restraint to one dimension and it
> looks to be fairly arbitrary.  I already suggested using the vector
> connecting the ligand COM with the binding site residues' COM and using
> that as pull_vec1.  Draw it out.  It makes a lot more sense than trying to
> restrain only along one axis, which as I have said before, makes no sense
> in this case.


As to obtain COM of ligand I'm using:  "g_traj_mpi -ox aco_com -com -s
npt.tpr" and taking the last frame's xy,z coordinate from the .xvg file
generated from that command.
 394 14.1362 14.4649 5.94131
 395 14.1435 14.45 5.94041
 396 14.0858 14.4461 5.90442
 397 14.1398 14.4164 5.86902
 398 14.1514 14.4434 5.8461
 399 14.1344 14.421 5.88976
 400 14.1996 14.4613 5.82814

Is this approach correct for taking COM?

Another question is that, how can I calculate COM for specific set of
residues ? If the above approach (for calculating Ligand COM) is correct
then it allows calculation of COM for whole protein only.
Please do suggest a way.



Thank you.



>
> -Justin
>
>
>>>