[gmx-users] Inconsistent shifts over periodic boundaries error.

[Artem Shekhovtsov]

Hello!
I performed simulations with the small molecules in water and faced
with the fact that in about 5% of cases, the simulation falls at the last
step with an error:

---
Program: gmx mdrun, version 2018.4
Source file: src/gromacs/pbcutil/mshift.cpp (line 906)

Fatal error:
There are inconsistent shifts over periodic boundaries in a molecule type
consisting of 47 atoms. The longest distance involved in such interactions
is
1.298 nm which is close to half the box length. This molecule type consists
of
multiple parts, e.g. monomers, that are connected by interactions that are
not
chemical bonds, e.g. restraints. Such systems can not be treated. The only
solution is increasing the box size.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
   The problem occurs when simulating in a rhombic dodecahedron cell with
the standard distance between solute and the box 1nm. There is no such
error in the cubic cell with distance 1nm.
Trying to establish the reason for this behavior, I found that it is
associated with the presence of virtual atoms in a small molecule. When I
exchange a virtual atom for an atom linked by a chemical bond to the rest
of the molecule, an error does not appear.

I want to remove errors while preserving virtual atoms as well as the
size and shape of the cell. Maybe someone already encountered this behavior
and knows what my mistake is. I will be glad of any help.

The link
https://drive.google.com/file/d/0B5NzD-LVrUalbDdSblhfTkowUDN1aWxER3hlLWhaRFROcjhj/view?usp=sharing
contains files for 1-step molecular dynamics that failed with my system of
interest. Gromacs version - 2018.4.

Thank you,
Artem Shekhovtsov
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Re: [gmx-users] Inconsistent Shifts

[Justin Lemkul]

On 2/25/18 6:27 PM, Dallas Warren wrote:

Iman,

As I mentioned earlier, does the warning actually stop the simulation
from running/completing?  If not, then simply ignore it.

One of the developers will need to chime in here about the error itself.


It would be helpful to know what exactly was being done beyond "using 
some commands in gromacs" to help here.


If it was an analysis tool, then there's no significance to this 
message, given the fact that there are periodic molecules. If it was 
from trjconv, again, we would have to know the *exact* command being used.


-Justin


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 25 February 2018 at 20:34, Iman Ahmadabadi
 wrote:

Dear Dallas,

I have tried the 2016.5 version of gromacs that it has the same warning
about the inconsistent shifts. I don't know why it should arises as a
warning and what is the problem. Is there another way to fix this warning?

Sincerely
Iman

On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:


Dear Dallas,

Yes, the system has periodic molecules (periodic-molecules = yes) and the
version of gromacs is 5.1.2. So, I should use for calculating the
properties of the system by gromacs 2016 and newer ones?

Respectfully,
Iman

On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:


Dear Gromacs users,

In using some commands in gromacs, the sentence "There were 240
inconsistent shifts. Check your topology" come up on the screen and I don't
know what is wrong in my topology file, however it calculates correctly the
features of the system but I would like to know the reason of this warning.

Respectfully,
Iman




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--
==

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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

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Re: [gmx-users] Inconsistent Shifts

[Dallas Warren]

Iman,

As I mentioned earlier, does the warning actually stop the simulation
from running/completing?  If not, then simply ignore it.

One of the developers will need to chime in here about the error itself.
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 25 February 2018 at 20:34, Iman Ahmadabadi
 wrote:
> Dear Dallas,
>
> I have tried the 2016.5 version of gromacs that it has the same warning
> about the inconsistent shifts. I don't know why it should arises as a
> warning and what is the problem. Is there another way to fix this warning?
>
> Sincerely
> Iman
>
> On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Dallas,
>>
>> Yes, the system has periodic molecules (periodic-molecules = yes) and the
>> version of gromacs is 5.1.2. So, I should use for calculating the
>> properties of the system by gromacs 2016 and newer ones?
>>
>> Respectfully,
>> Iman
>>
>> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
>> imanahmadabad...@gmail.com> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> In using some commands in gromacs, the sentence "There were 240
>>> inconsistent shifts. Check your topology" come up on the screen and I don't
>>> know what is wrong in my topology file, however it calculates correctly the
>>> features of the system but I would like to know the reason of this warning.
>>>
>>> Respectfully,
>>> Iman
>>>
>>
>>
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[gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Dallas,

I have tried the 2016.5 version of gromacs that it has the same warning
about the inconsistent shifts. I don't know why it should arises as a
warning and what is the problem. Is there another way to fix this warning?

Sincerely
Iman

On Wed, Feb 21, 2018 at 11:26 AM, Iman Ahmadabadi <
imanahmadabad...@gmail.com> wrote:

> Dear Dallas,
>
> Yes, the system has periodic molecules (periodic-molecules = yes) and the
> version of gromacs is 5.1.2. So, I should use for calculating the
> properties of the system by gromacs 2016 and newer ones?
>
> Respectfully,
> Iman
>
> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi <
> imanahmadabad...@gmail.com> wrote:
>
>> Dear Gromacs users,
>>
>> In using some commands in gromacs, the sentence "There were 240
>> inconsistent shifts. Check your topology" come up on the screen and I don't
>> know what is wrong in my topology file, however it calculates correctly the
>> features of the system but I would like to know the reason of this warning.
>>
>> Respectfully,
>> Iman
>>
>
>
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Re: [gmx-users] Inconsistent Shifts

[Dallas Warren]

Iman,

Updating to the latest version is always a good idea.

However, the warning you have gotten doesn't actually effect any
results you obtain from running the simulation.  You simulation still
gets completed, doesn't it?  So you can actually ignore it then, and
update to the latest versions of GROMACS at a later time as
needed/able.
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 21 February 2018 at 18:56, Iman Ahmadabadi
 wrote:
> Dear Dallas,
>
> Yes, the system has periodic molecules (periodic-molecules = yes) and the
> version of gromacs is 5.1.2. So, I should use for calculating the
> properties of the system by gromacs 2016 and newer ones?
>
> Respectfully,
> Iman
>
> On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi > wrote:
>
>> Dear Gromacs users,
>>
>> In using some commands in gromacs, the sentence "There were 240
>> inconsistent shifts. Check your topology" come up on the screen and I don't
>> know what is wrong in my topology file, however it calculates correctly the
>> features of the system but I would like to know the reason of this warning.
>>
>> Respectfully,
>> Iman
>>
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Re: [gmx-users] Inconsistent Shifts

[Iman Ahmadabadi]

Dear Dallas,

Yes, the system has periodic molecules (periodic-molecules = yes) and the
version of gromacs is 5.1.2. So, I should use for calculating the
properties of the system by gromacs 2016 and newer ones?

Respectfully,
Iman

On Tue, Feb 20, 2018 at 2:57 PM, Iman Ahmadabadi  wrote:

> Dear Gromacs users,
>
> In using some commands in gromacs, the sentence "There were 240
> inconsistent shifts. Check your topology" come up on the screen and I don't
> know what is wrong in my topology file, however it calculates correctly the
> features of the system but I would like to know the reason of this warning.
>
> Respectfully,
> Iman
>
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Re: [gmx-users] Inconsistent Shifts

[Dallas Warren]

What version of GROMACS are you using?  Do you have periodic molecules
in the system? i.e. periodic-molecules = yes in mdp file?

Known bug, that has been recently fixed.

https://redmine.gromacs.org/issues/2275
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 20 February 2018 at 22:27, Iman Ahmadabadi
 wrote:
> Dear Gromacs users,
>
> In using some commands in gromacs, the sentence "There were 240
> inconsistent shifts. Check your topology" come up on the screen and I don't
> know what is wrong in my topology file, however it calculates correctly the
> features of the system but I would like to know the reason of this warning.
>
> Respectfully,
> Iman
> --
> Gromacs Users mailing list
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> * Please search the archive at 
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Re: [gmx-users] Inconsistent shifts

[Mijiddorj Batsaikhan]

Dear Justin,

Thank you very much.

Best regards,

Mijiddorj

>
> On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote:
> > Dear Justin,
> >
> > Thank you very much for reply.
> > My commands
> >
> > gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump
> > gmx trjconv -s ../step7_1.tpr -f md_nojump.xtc -pbc mol  -ur compact -n
> > ../index.ndx -fit transxy -o md_noPBC.xtc
> >
> > I got the inconsistent shifts error middle of the trajectory.
> >
>
> Don't use -pbc and -fit simultaneously.  Do -pbc mol then do whatever
> fitting
> you want.  Simultaneously trying to re-wrap PBC and apply any sort of
> fitting is
> incompatible.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
>
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Re: [gmx-users] Inconsistent shifts

[Justin Lemkul]

On 12/14/16 11:13 AM, Mijiddorj Batsaikhan wrote:

Dear Justin,

Thank you very much for reply.
My commands

gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump
gmx trjconv -s ../step7_1.tpr -f md_nojump.xtc -pbc mol  -ur compact -n
../index.ndx -fit transxy -o md_noPBC.xtc

I got the inconsistent shifts error middle of the trajectory.



Don't use -pbc and -fit simultaneously.  Do -pbc mol then do whatever fitting 
you want.  Simultaneously trying to re-wrap PBC and apply any sort of fitting is 
incompatible.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Inconsistent shifts

[Mijiddorj Batsaikhan]

Dear Justin,

Thank you very much for reply.
My commands

gmx trjconv -s ../step7_1.tpr -f md.xtc -o md_nojump.xtc -pbc nojump
gmx trjconv -s ../step7_1.tpr -f md_nojump.xtc -pbc mol  -ur compact -n
../index.ndx -fit transxy -o md_noPBC.xtc

I got the inconsistent shifts error middle of the trajectory.

Best regards,

Mijiddorj


>
> --
>
> Message: 5
> Date: Wed, 14 Dec 2016 07:54:53 -0500
> From: Justin Lemkul <jalem...@vt.edu>
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Inconsistent shifts
> Message-ID: <c106ba53-7a82-6461-1414-171bfcec2...@vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> On 12/14/16 2:06 AM, Mijiddorj Batsaikhan wrote:
> > Dear gmx users,
> >
> > I simulated membrane and protein system. I would like to make analysis,
> and
> > during the removing periodicity, I got the inconsistent shifts fatal
> error.
> > How can fix this error? Can you help me?
> >
>
> Not without seeing your exact sequence of commands.
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
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Re: [gmx-users] Inconsistent shifts

[Justin Lemkul]

On 12/14/16 2:06 AM, Mijiddorj Batsaikhan wrote:

Dear gmx users,

I simulated membrane and protein system. I would like to make analysis, and
during the removing periodicity, I got the inconsistent shifts fatal error.
How can fix this error? Can you help me?



Not without seeing your exact sequence of commands.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Inconsistent shifts

[Mijiddorj Batsaikhan]

Dear gmx users,

I simulated membrane and protein system. I would like to make analysis, and
during the removing periodicity, I got the inconsistent shifts fatal error.
How can fix this error? Can you help me?

Best regards,

Mijiddorj
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[gmx-users] inconsistent shifts while using distance restraints

[Kortzak, Daniel]

Dear gmx-useres,

I am simulating a protein in a box with water and ions and now I am trying to 
keep the ions away from a particular residue of the protein. To do this I am 
using distance restraints. So I created a new molecule type with the protein 
and all ions and added distance restraints between each ion and the C-alpha of 
the residue in the protein. To get a repulsive flat-bottom distance restraint I 
set low to 0.9 nm and up1,up2 to 98, 99nm (box vectors are all around 15nm).
Everything seems to be working fine (in some 3000steps test simulations) but 
mdrun prints the message "There were inconsistent shifts." I guess this is 
because I have distance restraints between atoms that are further away from 
each other than half the shortest box vector, but since there is no force 
acting on those pairs I would not worry too much. So my questions are:
Is my guess correct?
Is there a better way than distance restraints too keep the ions away from 
their binding site?
Here I have to add that the protein is actually a dimer so I have two distance 
restraints per ion, that is the reason to choose distance restraints rather 
than position restraints.

cheers,
Daniel Kortzak




Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
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Prof. Dr. Sebastian M. Schmidt



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[gmx-users] Inconsistent shifts after switching form 4.5.7 to 5.0.4 version

[Mikhail Stukan]

Dear Gromacs users,

Good someone give me a hit about the following issue. I am running a system 
which contains few periodic molecules (graphene sheets). Everything was running 
fine when the simulations were performed using group cut-off scheme and GROMACS 
4.5.7. However, when I tried to transfer the same system to 5.0.4 version and 
switch from group to Verlet scheme the run crashed with the following error:
"There were 80 inconsistent shifts. Check your topology"

No changes in topology files were performed. The difference in MDP files 
between two cases is shown below. Am I doing something obviously wrong?

Many thanks in advance,
Mikhail

MDP-file for 5.0.4 (error about inconsistent shifts )

pbc =  xyz  ; periodic boundary conditions
cutoff-scheme   =  Verlet
verlet-buffer-drift =  0.005
;== Electrostatics
coulombtype =  PME
rcoulomb=  1.2  ; cut-off for coulomb
;== Van der Waals
vdw-type=  switch
rvdw_switch =  1.0
rvdw=  1.2  ; cut-off for vdw
;== EWALD/PME/PPPM parameters
fourierspacing  =  0.12
pme_order   =  6
ewald_rtol  =  1e-06
epsilon_surface =  0
optimize_fft=  yes  ; perform FFT optimization at start

old MDP-file for 4.5.7 (running without any trouble)

pbc =  xyz  ; periodic boundary conditions
periodic-molecules  =  yes  ; in the system present periodic 
molecules
rlist   =  1.5  ; cut-off for ns
;== Electrostatics
coulombtype =  PME
rcoulomb=  1.5  ; cut-off for coulomb
;== Van der Waals
vdw-type=  switch
rvdw_switch =  1.0
rvdw=  1.2  ; cut-off for vdw
;== EWALD/PME/PPPM parameters
fourierspacing  =  0.12
pme_order   =  6
ewald_rtol  =  1e-06
epsilon_surface =  0
optimize_fft=  yes  ; perform FFT optimization at start


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[gmx-users] inconsistent shifts warning

[sang eun jee]

Dear gromacs users

Hello.

I have question about inconsistent shifts warning when I am simulating
infinite peptide chains.

My system is (GLY-PRO-HYP)7 and I connected N atom of the first GLY residue
to the C atom of the last HYP atom. Therefore, the chain is
(N-CA-CO)-PRO-HYP-(GLY-PRO-HYP)5-GLY-PRO-(N-CD2-CG-CB-CA-CO) , while
N-CA-CO represents first GLY and N-CD2-CG-CB-CA-CO represents last HYP. N
of GLY is connected to the C of HYP via editing *.ftp, *.hdb and other
related forcefield files. specbond.dat was edited to include this specific
bond.

After editing forcefield, I processed structure with pdb2gmx and checked
all details of the bonds,pairs, dihedrals from topol.itp file that pdb2gmx
generated. I checked structure files with vmd visualizer and pdb visualizer
and confirmed the two atoms in each edge are close enough to form bond in
pbc condition.

In my system, NHCO protein bond between first GLY and last HYP crosses
periodic boundary.
So, I set *.mdp option as pdb=xyz, periodic_molecules =yes. Energy
minimization worked fine.
But, when I ran nvt  npt md, with and without constraining backbones, I
showed warning There were 2 inconsistent shifts. Check your topology.

When I checked the structure files,  C and O atoms from last HYP is
detached from the last part of the chain and attached to the first part of
the chain.
 (N-CA-CO)-PRO-HYP-(GLY-PRO-HYP)5-GLY-PRO-(N-CD2-CG-CB-CA-CO)
--  (CO)-(N-CA-CO)-PRO-HYP-(GLY-PRO-HYP)5-GLY-PRO-(N-CD2-CG-CB-CA)
And when I changed the number of chains to 3, then I could observe number
of inconsistent shifts are exactly consistent(6) with the number of C and O
atoms of HYP, which were moved to the first chains.

I searched archives and there were many reports related inconsistent shifts
warning, but none of them are related with my case. From careful
observation of the gromacs codes mshift.cpp, it looks like this warning is
printed when the position of the shifted atom by pbc is not consistent with
the designated position, but I cannot figure out more details.

If some of you have any idea or experience with this error, please help me.
I really appreciate it.

Sangeun Jee


-- 
Post Doctoral Researcher
School of Materials Science and Engineering
Georgia Institute of Technology
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