Re: [gmx-users] Periodic boundary conditions during the simulation

[Dallas Warren]

Boundaries of the box used for visualisation are totally arbitrary, it
makes not difference when the various simulations are being performed.
Most efficient to simply process it at the end to get the visual
representation you want

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 24 Apr 2020 at 12:29, Mohamed Abdelaal 
wrote:

> Hello everybody,
>
> I know that due to periodic boundary conditions the molecules move from one
> side of the box to the other side and moves outside the box. I also know
> how to use trjconv to solve this problem and I usually do this step at the
> end of the simulation. However I have noticed that after the energy
> minimization, some molecules which were position restrained at the bottom
> of the box have been moved to the top of the box. I knew that I have this
> periodic boundary condition problem not just from visualization of the
> structure after the energy minimization, but also from the atoms
> coordinates in the .gro file after the energy minimization, the z
> coordinate of some atoms have been changed from bottom to top as below:
>
> before energy minimization: (the z coordinate was always zero)
>
> 1GRM C11   0.061   0.071   0.000
> 1GRM C22   0.184   0.142   0.000
> 1GRM C33   0.184   0.284   0.000
> 1GRM C44   0.061   0.355   0.000
> 2GRM C15   0.061   0.497   0.000
>
>
> after energy minimization: (z coordinate of some atoms have been changed
> into 14 which is at the top of the box)
>
> 1GRM C11   0.061   0.071  14.000
> 1GRM C22   0.184   0.142  14.000
> 1GRM C33   0.184   0.284   0.000
> 1GRM C44   0.061   0.355   0.000
> 2GRM C15   0.061   0.497  14.000
>
>
>
> Do I need to solve this PBC problem between the different steps (energy
> min, NVT, NPT, production run) or it is okay to continue my simulation
> (even if the molecules have moved) and solve this problem at the end ?
>
> Many thanks,
> Mohamed
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[gmx-users] Periodic boundary conditions during the simulation

[Mohamed Abdelaal]

Hello everybody,

I know that due to periodic boundary conditions the molecules move from one
side of the box to the other side and moves outside the box. I also know
how to use trjconv to solve this problem and I usually do this step at the
end of the simulation. However I have noticed that after the energy
minimization, some molecules which were position restrained at the bottom
of the box have been moved to the top of the box. I knew that I have this
periodic boundary condition problem not just from visualization of the
structure after the energy minimization, but also from the atoms
coordinates in the .gro file after the energy minimization, the z
coordinate of some atoms have been changed from bottom to top as below:

before energy minimization: (the z coordinate was always zero)

1GRM C11   0.061   0.071   0.000
1GRM C22   0.184   0.142   0.000
1GRM C33   0.184   0.284   0.000
1GRM C44   0.061   0.355   0.000
2GRM C15   0.061   0.497   0.000


after energy minimization: (z coordinate of some atoms have been changed
into 14 which is at the top of the box)

1GRM C11   0.061   0.071  14.000
1GRM C22   0.184   0.142  14.000
1GRM C33   0.184   0.284   0.000
1GRM C44   0.061   0.355   0.000
2GRM C15   0.061   0.497  14.000



Do I need to solve this PBC problem between the different steps (energy
min, NVT, NPT, production run) or it is okay to continue my simulation
(even if the molecules have moved) and solve this problem at the end ?

Many thanks,
Mohamed
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Re: [gmx-users] Periodic Boundary Conditions

[Justin Lemkul]

On 2/10/19 12:26 PM, marzieh gharouni wrote:

Hello
I want to do noPeriodic Boundary Conditions for my system.
Gromacs tutorial has said that it can not be used the center and nojump in
one command simultaneously.
I would be grateful if you could explain the reasons for it?


Both apply translations to the coordinates, which are going to be in 
conflict with one another. The use of -pbc nojump allows atoms to appear 
to stray "outside" the box, but then trying to center them will try to 
move them back towards the middle of the box. These are mutually 
exclusive operations.


-Justin

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==

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Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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[gmx-users] Periodic Boundary Conditions

[marzieh gharouni]

Hello
I want to do noPeriodic Boundary Conditions for my system.
Gromacs tutorial has said that it can not be used the center and nojump in
one command simultaneously.
I would be grateful if you could explain the reasons for it?
please see this tutorial

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Thanks a lot.
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[gmx-users] periodic boundary conditions

[JAVAD MAHMOUDZADEH]

Dear Gromacs developers and usersI have three questions. I appreciate it if you 
answer them:
1)I am doing MD simulation on a bilayer. The problem I have encounteredis that 
either I do reimaging on the trajectory using –pbc mol –ur compact ornot, the 
number of Na ions in each leaflet is shown different when I check thetrajectory 
through VMD every 1000ps. I have 30 Na ions in my simulation boxwhich at the 
beginning of MD are distributed 15 on upper leaflet and 15 onlower leaflet. 
After 1 ns from the start of MD simulation, there is 9 Na ionson upper leaflet 
and 21 on lower leaflet. After 2 ns from the start of MDsimulation, there is 10 
Na ions on upper leaflet and 20 on lower leaflet. Thisis while when I check the 
movement of Na ions in VMD during the course ofsimulation, none of the Na ions 
cross the bilayer. Once I tracked the movementsof one of Na ions, I saw 
suddenly it disappeared from upper leaflet and appearedin lower leaflet. 
Therefore, I guess the problem should be related to the periodicboundary 
conditions (PBC). Why I see this uneven distribution of Na ions while Ihave 
used –pbc mol –ur compact?
2) As far as I know, when PBC is being used for MDsimulation, no reimaging is 
necessary (mandatory) to be done on the trajectorybefore the analysis are 
performed on the trajectory (unless if we want to havea nice image when we look 
in the system through VMD). On the other hand I knowthat what is written in the 
trajectory while MD simulation is being done, isthe coordinate of the atoms 
inside primary box and not atoms in periodic boxeseven those atoms which the 
atoms in primary cell are interacting with them. Howdoes Gromacs know the 
correct position of atoms which have already left the boxwhile the coordinates 
related to them (which have written to trajectory)belongs to their periodic 
images? For example, when you look at a trajectory inVMD (before reimaging), 
you see long unusual bonds from one side of the box toanother side. The reason 
is that for example one hydrogen atom of a watermolecule has left the box from 
right hand side and its periodic image hasentered from left hand side and since 
the position of this newly enteredhydrogen is written to trajectory we see long 
unusual bond across the boxbetween oxygen and hydrogen.  In case ofmy example 
on hydrogen atom, from the topology, Gromacs knows that for exampleO number 20 
is bonded to Hydrogen 21 so when reimaging is done the programknows that should 
bring back the H21 next to O20. But what about Na ions? Sincethey are not 
covalently bond to anywhere, how the program should know thatwhether the Na 
number 1233 (as an example) belongs to the upper leaflet orlower leaflet? 3- We 
know that to get correct data from analysis, every atomin each frame should 
have its correct position otherwise the analysis which aredone, produce wrong 
data. In one hand we know that reimaging is not necessary(mandatory) to be done 
on the trajectory before the analysis are performed on it.On the other hand we 
know that the coordinates written to the trajectory filefor the atoms which 
have left the box belongs to their periodic images that haveentered the box 
from other side and these coordinates do not show the realposition of those 
atoms taken into consideration while calculation of forcesand energy. Does the 
Gromacs itself do reimaging as part of each analyses beforethe analysis (for 
example calculation of number of Hbonds) is done? 
With RegardsJavad
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Re: [gmx-users] periodic boundary conditions

[Mark Abraham]

Hi,

On Wed, Jul 13, 2016 at 5:50 PM Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Hi Mark,
>
> Thanks for your reply.
>
> The 6 around 1 setup is also periodic.
>
> I understand this. However, we can argue the same for 6-1 system as well.
> Right?
>

Sure, but that's not the point. The point revolves around whether the
properties of your simulation system suitably resemble those found in the
real world. If that's a single cylinder of lipid suspended in some other
milieu, then neither of the periodic systems is particularly representative.


> If one edge of this hexagonal deforms, the other side also deforms and in
> fact we are applying a symmetry to our system.
>

Yeah, but only you know whether you are trying to study a
pseudo-crystalline form, or something else? The former is easier, because
you can accept periodicity as part of a model, but the conclusions may not
be applicable outside of that modelling regime...

Mark

The question is: which system is big enough (or suitable) to include this
> effect?
>
> What I am interested in is the structural properties of these systems and
> lipid-lipid interactions.
>
> Cheers
>
> On Wed, Jul 13, 2016 at 2:23 AM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > These are different systems. Your 6-around-1 setup (whether itself
> > hexagonally periodic or not) has degrees of freedom that the single
> > hexagonal cell cannot access. In the latter case, if a wall on one edge
> of
> > the cell deforms, then the corresponding wall on the far side of the cell
> > has the matching deformation. However the 6-around-1 can e.g. deform each
> > wall of the central hexagonal cell independently. Whether any of these
> make
> > a "correct" model depends what you're trying to model.
> >
> > Mark
> >
> > On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour <
> > ramezanpour.moh...@gmail.com> wrote:
> >
> > > Dear gromacs-users,
> > >
> > > Doing simulations on lipid HII phase, I came to a question which I
> could
> > > not get happy with my answer. I appreciate your opinion in advance:
> > >
> > > Imagine you have a cylinder made of lipids with waters only inside the
> > > cylinder, which is long enough and can be run for enough time so that
> > there
> > > is no problem from sampling aspect. A hexagonal pbc has been also
> applied
> > > to this cylinder properly.
> > >
> > > In the other system, you have 7 cyinders with 1 central and 6 on the
> > > corners of hexagon. The only main difference with the case above will
> be
> > a
> > > larger unit cell and less symmetry of the system.
> > >
> > > Do you expect the results of these two simulations be different, if you
> > are
> > > interested in structural properties?
> > >
> > > In other words: does pbc exactly treats the central cylinder as if
> there
> > > was 6 extra cylinders around the it? Can it reproduce the correct
> > > environment the central cylinder feels around?
> > >
> > > Cheer,
> > > Mohsen
> > >
> > >
> > >
> > > --
> > > *Rewards work better than punishment ...*
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
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> > >
> > --
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> >
>
>
>
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Re: [gmx-users] periodic boundary conditions

[Mohsen Ramezanpour]

Any other comment on this? :-)

On Wed, Jul 13, 2016 at 9:50 AM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Hi Mark,
>
> Thanks for your reply.
>
> The 6 around 1 setup is also periodic.
>
> I understand this. However, we can argue the same for 6-1 system as well.
> Right?
>
> If one edge of this hexagonal deforms, the other side also deforms and in
> fact we are applying a symmetry to our system.
>
> The question is: which system is big enough (or suitable) to include this
> effect?
>
> What I am interested in is the structural properties of these systems and
> lipid-lipid interactions.
>
> Cheers
>
> On Wed, Jul 13, 2016 at 2:23 AM, Mark Abraham 
> wrote:
>
>> Hi,
>>
>> These are different systems. Your 6-around-1 setup (whether itself
>> hexagonally periodic or not) has degrees of freedom that the single
>> hexagonal cell cannot access. In the latter case, if a wall on one edge of
>> the cell deforms, then the corresponding wall on the far side of the cell
>> has the matching deformation. However the 6-around-1 can e.g. deform each
>> wall of the central hexagonal cell independently. Whether any of these
>> make
>> a "correct" model depends what you're trying to model.
>>
>> Mark
>>
>> On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour <
>> ramezanpour.moh...@gmail.com> wrote:
>>
>> > Dear gromacs-users,
>> >
>> > Doing simulations on lipid HII phase, I came to a question which I could
>> > not get happy with my answer. I appreciate your opinion in advance:
>> >
>> > Imagine you have a cylinder made of lipids with waters only inside the
>> > cylinder, which is long enough and can be run for enough time so that
>> there
>> > is no problem from sampling aspect. A hexagonal pbc has been also
>> applied
>> > to this cylinder properly.
>> >
>> > In the other system, you have 7 cyinders with 1 central and 6 on the
>> > corners of hexagon. The only main difference with the case above will
>> be a
>> > larger unit cell and less symmetry of the system.
>> >
>> > Do you expect the results of these two simulations be different, if you
>> are
>> > interested in structural properties?
>> >
>> > In other words: does pbc exactly treats the central cylinder as if there
>> > was 6 extra cylinders around the it? Can it reproduce the correct
>> > environment the central cylinder feels around?
>> >
>> > Cheer,
>> > Mohsen
>> >
>> >
>> >
>> > --
>> > *Rewards work better than punishment ...*
>> > --
>> > Gromacs Users mailing list
>> >
>> > * Please search the archive at
>> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> > posting!
>> >
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
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>> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> > send a mail to gmx-users-requ...@gromacs.org.
>> >
>> --
>> Gromacs Users mailing list
>>
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>>
>
>
>
> --
> *Rewards work better than punishment ...*
>



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Re: [gmx-users] periodic boundary conditions

[Mohsen Ramezanpour]

Hi Mark,

Thanks for your reply.

The 6 around 1 setup is also periodic.

I understand this. However, we can argue the same for 6-1 system as well.
Right?

If one edge of this hexagonal deforms, the other side also deforms and in
fact we are applying a symmetry to our system.

The question is: which system is big enough (or suitable) to include this
effect?

What I am interested in is the structural properties of these systems and
lipid-lipid interactions.

Cheers

On Wed, Jul 13, 2016 at 2:23 AM, Mark Abraham 
wrote:

> Hi,
>
> These are different systems. Your 6-around-1 setup (whether itself
> hexagonally periodic or not) has degrees of freedom that the single
> hexagonal cell cannot access. In the latter case, if a wall on one edge of
> the cell deforms, then the corresponding wall on the far side of the cell
> has the matching deformation. However the 6-around-1 can e.g. deform each
> wall of the central hexagonal cell independently. Whether any of these make
> a "correct" model depends what you're trying to model.
>
> Mark
>
> On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour <
> ramezanpour.moh...@gmail.com> wrote:
>
> > Dear gromacs-users,
> >
> > Doing simulations on lipid HII phase, I came to a question which I could
> > not get happy with my answer. I appreciate your opinion in advance:
> >
> > Imagine you have a cylinder made of lipids with waters only inside the
> > cylinder, which is long enough and can be run for enough time so that
> there
> > is no problem from sampling aspect. A hexagonal pbc has been also applied
> > to this cylinder properly.
> >
> > In the other system, you have 7 cyinders with 1 central and 6 on the
> > corners of hexagon. The only main difference with the case above will be
> a
> > larger unit cell and less symmetry of the system.
> >
> > Do you expect the results of these two simulations be different, if you
> are
> > interested in structural properties?
> >
> > In other words: does pbc exactly treats the central cylinder as if there
> > was 6 extra cylinders around the it? Can it reproduce the correct
> > environment the central cylinder feels around?
> >
> > Cheer,
> > Mohsen
> >
> >
> >
> > --
> > *Rewards work better than punishment ...*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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Re: [gmx-users] periodic boundary conditions

[Mark Abraham]

Hi,

These are different systems. Your 6-around-1 setup (whether itself
hexagonally periodic or not) has degrees of freedom that the single
hexagonal cell cannot access. In the latter case, if a wall on one edge of
the cell deforms, then the corresponding wall on the far side of the cell
has the matching deformation. However the 6-around-1 can e.g. deform each
wall of the central hexagonal cell independently. Whether any of these make
a "correct" model depends what you're trying to model.

Mark

On Wed, Jul 13, 2016 at 2:41 AM Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear gromacs-users,
>
> Doing simulations on lipid HII phase, I came to a question which I could
> not get happy with my answer. I appreciate your opinion in advance:
>
> Imagine you have a cylinder made of lipids with waters only inside the
> cylinder, which is long enough and can be run for enough time so that there
> is no problem from sampling aspect. A hexagonal pbc has been also applied
> to this cylinder properly.
>
> In the other system, you have 7 cyinders with 1 central and 6 on the
> corners of hexagon. The only main difference with the case above will be a
> larger unit cell and less symmetry of the system.
>
> Do you expect the results of these two simulations be different, if you are
> interested in structural properties?
>
> In other words: does pbc exactly treats the central cylinder as if there
> was 6 extra cylinders around the it? Can it reproduce the correct
> environment the central cylinder feels around?
>
> Cheer,
> Mohsen
>
>
>
> --
> *Rewards work better than punishment ...*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] periodic boundary conditions

[Mohsen Ramezanpour]

Dear gromacs-users,

Doing simulations on lipid HII phase, I came to a question which I could
not get happy with my answer. I appreciate your opinion in advance:

Imagine you have a cylinder made of lipids with waters only inside the
cylinder, which is long enough and can be run for enough time so that there
is no problem from sampling aspect. A hexagonal pbc has been also applied
to this cylinder properly.

In the other system, you have 7 cyinders with 1 central and 6 on the
corners of hexagon. The only main difference with the case above will be a
larger unit cell and less symmetry of the system.

Do you expect the results of these two simulations be different, if you are
interested in structural properties?

In other words: does pbc exactly treats the central cylinder as if there
was 6 extra cylinders around the it? Can it reproduce the correct
environment the central cylinder feels around?

Cheer,
Mohsen



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Re: [gmx-users] periodic boundary conditions pbc=xyz

[Tushar Ranjan Moharana]

Hi Ming
Use *-pbc mol* while using trjconv. Anyway it is not another box.

Best Regards
-- 
Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB, INDIA
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[gmx-users] periodic boundary conditions pbc=xyz

[Ming Tang]

Dear all,

I did a simulation using periodic boundary conditions pbc=xyz. It turns out 
that the box is defined too small, and some atoms go to another box.
Does this affect the simulation result? If not, how to display the real model 
(without separation) in VMD?

Thanks in advance,
Ming
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Re: [gmx-users] periodic boundary conditions pbc=xyz

[Tsjerk Wassenaar]

Hi Ming,

You have another box in your (infinite) periodic system?

Cheers,

Tsjerk


On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear all,

 I did a simulation using periodic boundary conditions pbc=xyz. It turns
 out that the box is defined too small, and some atoms go to another box.
 Does this affect the simulation result? If not, how to display the real
 model (without separation) in VMD?

 Thanks in advance,
 Ming
 --
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 http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
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Re: [gmx-users] periodic boundary conditions pbc=xyz

[Ming Tang]

Hi Tsjerk,

I defined only one box. I mean several atoms in one chain run out of the 
boundary, and I can see them in the box but not in the chain. So I think maybe 
they run to the nearby box because of the periodic boundary conditions.

Thanks,
Ming 

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Tsjerk 
Wassenaar
Sent: Sunday, 5 April 2015 7:43 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] periodic boundary conditions pbc=xyz

Hi Ming,

You have another box in your (infinite) periodic system?

Cheers,

Tsjerk


On Sun, Apr 5, 2015 at 10:32 AM, Ming Tang m21.t...@qut.edu.au wrote:

 Dear all,

 I did a simulation using periodic boundary conditions pbc=xyz. It 
 turns out that the box is defined too small, and some atoms go to another box.
 Does this affect the simulation result? If not, how to display the 
 real model (without separation) in VMD?

 Thanks in advance,
 Ming
 --
 Gromacs Users mailing list

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Tsjerk A. Wassenaar, Ph.D.
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