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

Magnus Lundborg magnus.lundborg at scilifelab.se
Mon Apr 27 13:22:25 CEST 2020 

Hi,

On 2020-04-24 20:32, Alex wrote:
> Hi Magnus,
> I see, many thanks for the  insights.
>
>
> On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg <
> magnus.lundborg at scilifelab.se> wrote:
>
>> Hi Alex,
>>
>> pull-group1-pbcatom lets you specify the exact atom used as the PBC
>> reference. Both 0 and -1 are special cases. For small molecules 0 is
>> (almost?) always OK. Find one in the center of you membrane (in the pull
>> direction). I'll actually have to check if -1 is even compatible with
>> pull-pbc-ref-prev-step-com. It's possible that that combination should
>> not be allowed even.
>>
> So, the pull-group1-pbcatm could be any other number as atom number rather
> than 0 and -1.

Yes, pick an atom located centrally in the structure.

>
>> As you say, you can define a subgroup within the larger membrane group,
>> but that is mainly of use if you know that some atoms consistently in
>> the center of the whole group and others are more flexible.
>>
> In this case where the subgroup defined in index.ndx file has more than one
> atom e.g. 30 atoms, which one of the atom in subgroup should be assigned to
> the pull-group1-pbcatom?
> If I am not mistaken, here, the entry number in index.ndx file belong to
> the subgroup should be assigned to the pull-group1-pbcatom.
>
> [ system ]
> [ Other ]
> ....
> [ non-water ]
> [ subgroup ]
>
> Would you please confirm if I am correct?

Yes, pick one atom from that subgroup, the atom should be centrally 
placed (at least not so far away that the COM of the pull group could be 
wrongly calculated). In almost all cases any atom should work (and in 
those cases using '0' should work as well, but makes it less transparent 
regarding what atom is used). With "pull-pbc-ref-prev-step-com" the 
specified atom is only used to set the PBC initially. After that the COM 
of the previous step is used, making it less sensitive if the chosen 
atom is very mobile.

Cheers,

Magnus

>
> Thank you
> Alex
>
>
>> Regards,
>>
>> Magnus
>>
>> On 2020-04-21 16:24, Alex wrote:
>>> Hi Magnus,
>>> Actually I am confused with the available options for the
>>> "pull-pbc-ref-prev-step-com"  and "pull-group1-pbcatom".
>>> For pull-pbc-ref-prev-step-com : YES or NO: where YES should be used when
>>> one of the group is large, even the 2020.1 version of grmacs would give a
>>> warning if one used No in a case of presence of a large group.
>>> Also, for the pull-group1-pbcatom: there are two options of 0 or -1. By 0
>>> the middle atom (number wise) of the large group is used automatically
>>> which is safe only for small groups as manual states. So, only
>>> remaining option is -1.
>>> So, what I understood for a layered-large group similar to what I have
>> one
>>> should use pull-pbc-ref-prev-step-com = YES and pull-group1-pbcatom = -1
>>> which would cause moving the system along -Z during the pulling.
>>>
>>> Using gmx select, can I manually define a sub-group around the COM of the
>>> large group, and consider it as one of the pulling groups instead of the
>>> large group?
>>>
>>> Thank you
>>> Alex
>>>
>>> On Mon, Apr 20, 2020 at 8:46 AM Magnus Lundborg <
>>> magnus.lundborg at scilifelab.se> wrote:
>>>
>>>> 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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