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

2020-04-27 Thread Magnus Lundborg

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.lundb...@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.lundb...@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.lundb...@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-r

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

2020-04-24 Thread Alex
Hi Magnus,
I see, many thanks for the  insights.


On Thu, Apr 23, 2020 at 2:45 AM Magnus Lundborg <
magnus.lundb...@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.

>
> 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?

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.lundb...@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.lundb...@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 

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

2020-04-22 Thread Magnus Lundborg

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.


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.


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.lundb...@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.lundb...@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 = 

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

2020-04-21 Thread Alex
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.lundb...@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.lundb...@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
>  -
> >

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

2020-04-20 Thread 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.lundb...@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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Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

2020-04-20 Thread Alex
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.lundb...@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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> * Please search the archive at
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Re: [gmx-users] Artifact in pull-pbc-ref-prev-step-com

2020-04-20 Thread 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





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

2020-04-20 Thread Magnus Lundborg

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

2020-04-19 Thread Alex
Any comment on this would be so appreciated!

Regards,
Alex

On Sat, Apr 18, 2020 at 2:12 PM 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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