Topology does not have beads of type "A"

[shu zong]

Dear teacher, hello. I was calculating the propane example, and I ran into a problem. The "Topology does not have beads of type "A" "error occurs when calculating the RDF of the objective function. Please help me to see if there is something wrong with the xml and top files

[Christoph Junghans]

On Mon, Nov 27, 2023 at 7:30 AM shu zong <qingc...@gmail.com> wrote:

Dear teacher, hello. I was calculating the propane example, and I ran into a problem. The "Topology does not have beads of type "A" "error occurs when calculating the RDF of the objective function. Please help me to see if there is something wrong with the xml and top files

I think you are mixing two things up!

Your gromacs topology is at the coarse-grained level, but your mapping file is for the atomistic level.

An example for everything atomistic can be found here: 

https://github.com/votca/votca/tree/master/csg-tutorials/propane/atomistic 

an example for everything coarse-grained is here:

https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi

Christoph

PS: please do NOT put screenshots in the email, they are not searchable and hence won't be very useful for other users with a similar issue.

Instead, attach the input files and copy error messages into the email directly.

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[shu zong]

Thank you very much for your reply. 

Through the teacher's explanation, I realized my mistake. The command I used earlier was "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml", Among them, topol.tpr and traj.trr are atomic files.

 Now I convert the trace file traj.trr with the command "csg_map --top topol.tpr --trj traj.trr --cg propane.xml --out traj_cg.trr". 

But when I use "csg_stat --top topol.tpr --trj traj_cg.trr --cg propane.xml --options settings.xml" again, I still say that the top file is faulty.

The problem is "to begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 3
Reading file topol.tpr, VERSION 2020.1 (single precision)
I have 11000 beads in 1000 molecules
I have 3000 beads in 1000 molecules for the coarsegraining
trr version: GMX_trn_file (double precision)
Reading frame 0 time 0.000
an error occurred:
number of beads in trajectory do not match topology
"

My top file is still the email from Creep

[Christoph Junghans]

On Tue, Nov 28, 2023 at 5:56 AM shu zong <qingc...@gmail.com> wrote:

Thank you very much for your reply. 

Through the teacher's explanation, I realized my mistake. The command I used earlier was "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml", Among them, topol.tpr and traj.trr are atomic files.

 Now I convert the trace file traj.trr with the command "csg_map --top topol.tpr --trj traj.trr --cg propane.xml --out traj_cg.trr". 

But when I use "csg_stat --top topol.tpr --trj traj_cg.trr --cg propane.xml --options settings.xml" again, I still say that the top file is faulty.

With a mapping file, please use the atomistic topology and trajectory here, e.g.:

$ csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml

Christoph

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[shu zong]

Thank you very much for your reply. The first email I sent was with this command, "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml." However, the "Topology does not have beads of type "A" "error is displayed。

I'm using this example.

 an example for everything coarse-grained is here:

https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi

test/ibi$ csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml

begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 3
Reading file topol.tpr, VERSION 2020.1 (single precision)
I have 11000 beads in 1000 molecules
I have 3000 beads in 1000 molecules for the coarsegraining

trr version: GMX_trn_file (single precision)

Reading frame       0 time    0.000  
an error occurred:

Topology does not have beads of type "A"

This was specified in type1 of interaction "A-A"
xuqch@chasing:~/simulation/Xuqch/test/ibi$ 

[Christoph Junghans]

On Thu, Nov 30, 2023 at 12:48 AM shu zong <qingc...@gmail.com> wrote:

Thank you very much for your reply. The first email I sent was with this command, "csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml." However, the "Topology does not have beads of type "A" "error is displayed。

I'm using this example.

 an example for everything coarse-grained is here:

https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi

test/ibi$ csg_stat --top topol.tpr --trj traj.trr --cg propane.xml --options settings.xml

This is an IBI tutorial, which is already on the coarse-grained level hence you don't need to specify a mapping file (--cg option) as there is nothing to map.

To run IBI just use csg_inverse (see run.sh).

See this tutorial on how to do IBI:

https://www.votca.org/csg-tutorials/Tutorial.html#iterative-boltzmann-inversion-ibi-for-spc-e-water

Christoph

 

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[shu zong]

Thank you very much for your reply. This issue has been successfully resolved, mainly with the inconsistency of the atomic names of several files. 

When I went to the next step to find ibi, a new problem arose.

“Fatal error:

The group cutoff scheme has been removed since GROMACS 2020. Please use the
Verlet cutoff scheme.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

# ERROR:                                                                                         # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro' failed #

# For details see the logfile /home/xuqch/simulation/Xuqch/test/ibi/inverse.log

”

How do I modify the mdp file？

Thank you very much

[Christoph Junghans]

On Fri, Dec 1, 2023 at 6:50 AM shu zong <qingc...@gmail.com> wrote:

Thank you very much for your reply. This issue has been successfully resolved, mainly with the inconsistency of the atomic names of several files. 

To support other users, how did you fix it?

 

When I went to the next step to find ibi, a new problem arose.

“Fatal error:

The group cutoff scheme has been removed since GROMACS 2020. Please use the
Verlet cutoff scheme.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

# ERROR:                                                                                         # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr -c conf.gro' failed #

# For details see the logfile /home/xuqch/simulation/Xuqch/test/ibi/inverse.log

”

How do I modify the mdp file？

Like I said in my email on Nov 2nd, for tabulated interactions you will need to use gromacs-2019.

Gromacs-2020, which you are using, doesn't support that feature anymore.

Alternatively you can lammps.  

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[shu zong]

I re-downloaded the 2019 version and it seems that the group is not recognized. 

Is it that I need to manually define groups A and B

“ Fatal error:
Group A referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors  ”

[Christoph Junghans]

On Fri, Dec 1, 2023 at 7:59 AM shu zong <qingc...@gmail.com> wrote:

I re-downloaded the 2019 version and it seems that the group is not recognized. 

Is it that I need to manually define groups A and B

I am not sure what are trying to do, but if you run the tutorial csg_inverse (via run.sh), it will

run grompp with the index file (gmx grompp -n index.ndx .....) automatically

(https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/index.ndx)

Christoph

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