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

[Magnus Lundborg]

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
>
>