[gmx-users] Artifact in pull-pbc-ref-prev-step-com

[Magnus Lundborg]

Hi Alex,

I don't see why it would need pull-group1-pbcatom = -1. Why not pick a 
central atom?

Regards,

Magnus

On 2020-04-20 13:40, Alex wrote:
> Hi Magnus,
> Thanks.
> The problem raises only because of using the pull-pbc-ref-prev-step-com
> which needs the pull-group1-pbcatom to be -1 to be meaningful.
> For an identical system and mdp parameters using 2018 version of gromacs
> which is independent to the pull-pbc-ref-prev-step-com, I see no issue.
>
> Regards,
> Alex
>
> On Mon, Apr 20, 2020 at 3:27 AM Magnus Lundborg <
> magnus.lundborg at scilifelab.se> wrote:
>
>> Sorry, about the statement about pbcatom -1. I was thinking about 0. I
>> don't know if pbcatom -1 is good or not in this case.
>>
>> Regards,
>>
>> Magnus
>>
>> On 2020-04-20 09:24, Magnus Lundborg wrote:
>>> Hi Alex,
>>>
>>> I don't think this is related to using pull-pbc-ref-prev-step-com.
>>> Have you tried without it? However, it is risky using pbcatom -1,
>>> since you don't know what atom you are using as the initial reference.
>>> I would suggest picking an atom you know is located at the centre of
>>> the structure.
>>>
>>> I would think that the problem has to do with the comm removal. What
>>> are your parameters for comm-mode, nstcomm and comm-grps? It is
>>> possible that you need to lower your nstcomm. It is also possible, but
>>> not certain, the comm-mode Linear-acceleration-correction might help
>>> you. For some reason, it seems like I have sometimes avoided similar
>>> problems by using the sd integrator instead, but I haven't evaluated
>>> that properly - it might just have been coincidences. If you see a
>>> clear difference using the sd integrator it might be good if you'd
>>> file an issue about it on gitlab so that someone can look into if
>>> there is something wrong.
>>>
>>> Regards,
>>> Magnus
>>>
>>> On 2020-04-18 20:12, Alex wrote:
>>>> Dear all,
>>>> To generate the initial configurations for umbrella sampling, I
>>>> conducted a
>>>> simple pulling simulation by which a single-small molecule (mol_A) is
>>>> being
>>>> dragged along -Z from water into the body of a thin film.
>>>> Since the thin film is large I used *"pull-pbc-ref-prev-step-com =
>>>> yes" and
>>>> "pull-group1-pbcatom      = -1"*  which cause a net shifting of the
>>>> system
>>>> along the pulling direction as soon as the mol_A reach to the thin film,
>>>> please find below the pulling flags movie and  plot in below links.
>>>>
>>>> Centering the thin film and mol_A could solve the issue,  (echo 1 0 |
>>>> trjconv -center yes) to some extent but still COM changes in the early
>>>> stage below 2ns. ,
>>>> COM:
>>>> https://drive.google.com/open?id=1-EcnV1uSu0I3eqdvjuUf2OxTZEXFD5m0
>>>>
>>>> Movie in which the water molecules are hidden:
>>>> https://drive.google.com/open?id=1gP5GBgfGYMithrA1o1T_RzlSdCS91gkv
>>>>
>>>> -
>>>> gmx version 2020.1
>>>> -----
>>>> pull                     = yes
>>>> pull-print-com           = no
>>>> pull-print-ref-value     = yes
>>>> pull-print-components    = Yes
>>>> pull-nstxout             = 1000
>>>> pull-nstfout             = 1000
>>>> pull-pbc-ref-prev-step-com = yes
>>>> pull-ngroups             = 2
>>>> pull-ncoords             = 1
>>>> pull-group1-name         = Thin-film
>>>> pull-group1-pbcatom      = -1
>>>> pull-group2-name         = mol_A
>>>> pull-group2-pbcatom      = 0
>>>> pull-coord1-type         = umbrella
>>>> pull-coord1-geometry     = direction
>>>> pull-coord1-groups       = 1 2
>>>> pull-coord1-dim          = N N Y
>>>> pull-coord1-origin       = 0.0 0.0 0.0
>>>> pull-coord1-vec          = 0.0 0.0 -1.0
>>>> pull-coord1-start        = yes
>>>> pull-coord1-init         = 0
>>>> pull-coord1-rate         = 0.0005
>>>> pull-coord1-k            = 5000
>>>> -----
>>>> I wonder if I could extract correct initial configuration from this
>>>> trajectory? With correct initial configuration, I mean a set of gro
>>>> file in
>>>> which change from one from to another is the distance between the COM of
>>>> the thin-film and mol_A?
>>>>
>>>> Thank you
>>>> Alex
>>>
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