Re: [gmx-users] Domain decomposition error with -rerun

[Nikhil Maroli]

Check the trajectories before and after conversion and make sure that there
are no pbc effect, if so fix it.
Or do the analysis with the avaible trajectories(may be in VMD with tcl
scripts).

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Regards,
Nikhil Maroli
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Re: [gmx-users] Domain decomposition error with -rerun

[Sahithya S Iyer]

Thanks for the reply Mark.

On Sat, Apr 28, 2018 at 4:32 PM, Mark Abraham 
wrote:

> Hi,
>
> Clearly the conversion tool did not produce a file that conforms to the
> requirements GROMACS has for specifying periodic boxes. That may not work
> well even if you'd run mdrun without domain decomposition because the
> periodicity may not be understood correctly. Find out what was going on and
> how the conversion may have worked.
>
> Mark
>
> On Sat, Apr 28, 2018, 09:54 Sahithya S Iyer  wrote:
>
> > Yes.. I used VMD for conversion...
> >
> > On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH 
> > wrote:
> >
> > > Hi
> > >
> > > Sounds strange to my little knowledge. How I would justify is, it may
> be
> > > due to the conversion from NAMD [dcd] to Gromacs profile [trr] though
> not
> > > sure.
> > >
> > > So you have converted the file format using VMD?
> > >
> > >
> > >
> > > On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer 
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > Thanks for the reply. I am only doing a rerun of a trajectory that
> has
> > > > already evolved without any dynamic load balancing problems.
> > > > -rerun only recalculates energies right. I don't understand why the
> > same
> > > > trajectory is giving decomposition error now.
> > > >
> > > > On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH <
> > drrahulsur...@gmail.com>
> > > > wrote:
> > > >
> > > > > Hi.
> > > > >
> > > > > That indicates a  problem with dynamic load balancing. Try to build
> > > > > different sizes of the box.
> > > > >
> > > > > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer <
> sah2...@gmail.com
> > >
> > > > > wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > > I am trying to calculate interaction between specific residues
> > using
> > > > gmx
> > > > > > mdrun -rerun flag. The trajectory was in a dcd format, which I
> > > > converted
> > > > > to
> > > > > > a trr file. I get the following error -
> > > > > >
> > > > > > Domain decomposition has not been implemented for box vectors
> that
> > > have
> > > > > > non-zero components in directions that do not use domain
> > > decomposition:
> > > > > > ncells
> > > > > > = 1 8 1, box vector[2] = 0.00 10.536000 0.00
> > > > > >
> > > > > > Can someone please tell me what could be going wrong here ?
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul Suresh*
> > > > > *Research Scholar*
> > > > > *Bharathiar University*
> > > > > *Coimbatore*
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
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> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
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> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
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> > > >
> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > Gromacs Users mailing list
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> * 

Re: [gmx-users] Domain decomposition error with -rerun

[Mark Abraham]

Hi,

Clearly the conversion tool did not produce a file that conforms to the
requirements GROMACS has for specifying periodic boxes. That may not work
well even if you'd run mdrun without domain decomposition because the
periodicity may not be understood correctly. Find out what was going on and
how the conversion may have worked.

Mark

On Sat, Apr 28, 2018, 09:54 Sahithya S Iyer  wrote:

> Yes.. I used VMD for conversion...
>
> On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH 
> wrote:
>
> > Hi
> >
> > Sounds strange to my little knowledge. How I would justify is, it may be
> > due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not
> > sure.
> >
> > So you have converted the file format using VMD?
> >
> >
> >
> > On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer 
> > wrote:
> >
> > > Hi,
> > >
> > > Thanks for the reply. I am only doing a rerun of a trajectory that has
> > > already evolved without any dynamic load balancing problems.
> > > -rerun only recalculates energies right. I don't understand why the
> same
> > > trajectory is giving decomposition error now.
> > >
> > > On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH <
> drrahulsur...@gmail.com>
> > > wrote:
> > >
> > > > Hi.
> > > >
> > > > That indicates a  problem with dynamic load balancing. Try to build
> > > > different sizes of the box.
> > > >
> > > > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer  >
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > I am trying to calculate interaction between specific residues
> using
> > > gmx
> > > > > mdrun -rerun flag. The trajectory was in a dcd format, which I
> > > converted
> > > > to
> > > > > a trr file. I get the following error -
> > > > >
> > > > > Domain decomposition has not been implemented for box vectors that
> > have
> > > > > non-zero components in directions that do not use domain
> > decomposition:
> > > > > ncells
> > > > > = 1 8 1, box vector[2] = 0.00 10.536000 0.00
> > > > >
> > > > > Can someone please tell me what could be going wrong here ?
> > > > > --
> > > > > 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
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > *Regards,*
> > > > *Rahul Suresh*
> > > > *Research Scholar*
> > > > *Bharathiar University*
> > > > *Coimbatore*
> > > > --
> > > > 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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> > > > 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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> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
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Re: [gmx-users] Domain decomposition error with -rerun

[Sahithya S Iyer]

Yes.. I used VMD for conversion...

On Sat, Apr 28, 2018 at 12:50 PM, RAHUL SURESH 
wrote:

> Hi
>
> Sounds strange to my little knowledge. How I would justify is, it may be
> due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not
> sure.
>
> So you have converted the file format using VMD?
>
>
>
> On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer 
> wrote:
>
> > Hi,
> >
> > Thanks for the reply. I am only doing a rerun of a trajectory that has
> > already evolved without any dynamic load balancing problems.
> > -rerun only recalculates energies right. I don't understand why the same
> > trajectory is giving decomposition error now.
> >
> > On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH 
> > wrote:
> >
> > > Hi.
> > >
> > > That indicates a  problem with dynamic load balancing. Try to build
> > > different sizes of the box.
> > >
> > > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer 
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I am trying to calculate interaction between specific residues using
> > gmx
> > > > mdrun -rerun flag. The trajectory was in a dcd format, which I
> > converted
> > > to
> > > > a trr file. I get the following error -
> > > >
> > > > Domain decomposition has not been implemented for box vectors that
> have
> > > > non-zero components in directions that do not use domain
> decomposition:
> > > > ncells
> > > > = 1 8 1, box vector[2] = 0.00 10.536000 0.00
> > > >
> > > > Can someone please tell me what could be going wrong here ?
> > > > --
> > > > 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
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > > *Regards,*
> > > *Rahul Suresh*
> > > *Research Scholar*
> > > *Bharathiar University*
> > > *Coimbatore*
> > > --
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > 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
> >
> > * Please search the archive at http://www.gromacs.org/
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> >
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> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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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[gmx-users] Dihedral parameters from QM and MM relaxed surface scans

[Eric Smoll]

Hello Gromacs Users,

I am trying to reproduce some published forcefield development work. In
this paper, dihedral parameters are derived from QM and MM relaxed surface
scan data collected on individual small molecules in vacuum.

My replication workflow is as follows. The MM relaxed surface scan
trajectory was prepared by concatenating the final frame of a set of energy
minimization calculations. Each energy minimization held the dihedral of
interest at a desired angle with a 1000 kJ/mol dihedral restraint. Other
DOF's were allowed to relax with the "steep" algorithm in single-precision
GROMACS 2018.1 to machine precision. A "restrained" dihedral PES was
calculated by collecting the molecule's potential as a function of dihedral
angle *with the restraint on the dihedral of interest*.

An "unrestrained" dihedral PES was also calculated by removing the dihedral
restraint on the dihedral of interest and calculating the energy with the
rerun feature of mdrun.

I find that the "restrained" MM dihedral PES is in excellent quantitative
agreement with QM relaxed surface scan data. The "unrestrained" MM dihedral
PES is only in qualitative agreement with the QM results. Peaks and dips in
the "unrestrained" PES are exaggerated when compared to the "restrained"
PES.

As far as I understand, the "unrestrained" PES should be more
appropriate/accurate than the "restrained" PES. Am I correct? Is there a
flaw in my workflow?

Best,
Eric
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Re: [gmx-users] Domain decomposition error with -rerun

[RAHUL SURESH]

Hi

Sounds strange to my little knowledge. How I would justify is, it may be
due to the conversion from NAMD [dcd] to Gromacs profile [trr] though not
sure.

So you have converted the file format using VMD?



On Sat, Apr 28, 2018 at 12:26 PM, Sahithya S Iyer  wrote:

> Hi,
>
> Thanks for the reply. I am only doing a rerun of a trajectory that has
> already evolved without any dynamic load balancing problems.
> -rerun only recalculates energies right. I don't understand why the same
> trajectory is giving decomposition error now.
>
> On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH 
> wrote:
>
> > Hi.
> >
> > That indicates a  problem with dynamic load balancing. Try to build
> > different sizes of the box.
> >
> > On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer 
> > wrote:
> >
> > > Hi,
> > >
> > > I am trying to calculate interaction between specific residues using
> gmx
> > > mdrun -rerun flag. The trajectory was in a dcd format, which I
> converted
> > to
> > > a trr file. I get the following error -
> > >
> > > Domain decomposition has not been implemented for box vectors that have
> > > non-zero components in directions that do not use domain decomposition:
> > > ncells
> > > = 1 8 1, box vector[2] = 0.00 10.536000 0.00
> > >
> > > Can someone please tell me what could be going wrong here ?
> > > --
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > 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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>
> * Please search the archive at http://www.gromacs.org/
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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Re: [gmx-users] Domain decomposition error with -rerun

[Sahithya S Iyer]

Hi,

Thanks for the reply. I am only doing a rerun of a trajectory that has
already evolved without any dynamic load balancing problems.
-rerun only recalculates energies right. I don't understand why the same
trajectory is giving decomposition error now.

On Sat, Apr 28, 2018 at 12:11 PM, RAHUL SURESH 
wrote:

> Hi.
>
> That indicates a  problem with dynamic load balancing. Try to build
> different sizes of the box.
>
> On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer 
> wrote:
>
> > Hi,
> >
> > I am trying to calculate interaction between specific residues using gmx
> > mdrun -rerun flag. The trajectory was in a dcd format, which I converted
> to
> > a trr file. I get the following error -
> >
> > Domain decomposition has not been implemented for box vectors that have
> > non-zero components in directions that do not use domain decomposition:
> > ncells
> > = 1 8 1, box vector[2] = 0.00 10.536000 0.00
> >
> > Can someone please tell me what could be going wrong here ?
> > --
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> 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
>
> * For (un)subscribe requests visit
> 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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Re: [gmx-users] Domain decomposition error with -rerun

[RAHUL SURESH]

Hi.

That indicates a  problem with dynamic load balancing. Try to build
different sizes of the box.

On Sat, Apr 28, 2018 at 11:57 AM, Sahithya S Iyer  wrote:

> Hi,
>
> I am trying to calculate interaction between specific residues using gmx
> mdrun -rerun flag. The trajectory was in a dcd format, which I converted to
> a trr file. I get the following error -
>
> Domain decomposition has not been implemented for box vectors that have
> non-zero components in directions that do not use domain decomposition:
> ncells
> = 1 8 1, box vector[2] = 0.00 10.536000 0.00
>
> Can someone please tell me what could be going wrong here ?
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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[gmx-users] Domain decomposition error with -rerun

[Sahithya S Iyer]

Hi,

I am trying to calculate interaction between specific residues using gmx
mdrun -rerun flag. The trajectory was in a dcd format, which I converted to
a trr file. I get the following error -

Domain decomposition has not been implemented for box vectors that have
non-zero components in directions that do not use domain decomposition:
ncells
= 1 8 1, box vector[2] = 0.00 10.536000 0.00

Can someone please tell me what could be going wrong here ?
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