Coulomb interactions

[MohaddesehPeyro]

Hello,

I previously asked a question here you regarding running Gromacs-FDA for a coarse-grained model. I successfully ran Gromacs-FDA with my files but now I have a question about getting .psa files for coulombic interactions. When I choose coulomb as the interaction type, I get 0 for all the values in the .psa file. I don't have this issue with other interaction types. Can you please help me with this?

Thanks, Mohaddeseh

[BerndDoser]

Yes, of course. Can you please provide me your in- and output files and the exact FDA version number, that I can try to reproduce your issue.

[BerndDoser]

Hi Mohaddeseh,

thank you for sending your files via email. Your GROMACS version 5.1.2 is pretty old and unfortunately not supported by FDA anymore. Please update your GROMACS to v2018 or v2019 and use the latest version of FDA 2.9.1.

Cheers, Bernd

[MohaddesehPeyro]

Hi Bernd,

I installed and used gromacs and fda 2018 and I still face the same issue. If you look at the output files (fda.psa) for coulomb interactions, it is all zeros. I sent you the new files via email. Can you please help with this?

Thanks, Mohaddeseh

On Tue, Sep 17, 2019 at 11:49 PM Bernd Doser notifications@github.com wrote:

Hi Mohaddeseh,

thank you for sending your files via email. Your GROMACS version 5.1.2 is pretty old and unfortunately not supported by FDA anymore. Please update your GROMACS to v2018 or v2019 and use the latest version of FDA 2.9.1.

Cheers, Bernd

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

Hi Mohaddeseh,

Yes, I will take a look. Only to be sure: You have taken the latest version v2018.7-fda2.9.1 and the trajectory was produced with the same gromacs version?

[MohaddesehPeyro]

Hi Bernd,

Thanks very much. The files in the new folder I sent you are all generated with the gromacs and gromacs-fda versions you mentioned except for the trajectory file. The trajectory file was produced with gromacs 5.1.2. I currently can't reproduce the trajectories with the recent version of gromacs due to some server issues. Would you be able to help with the current files?

Best, Mohaddeseh

On Tue, Sep 24, 2019 at 1:17 PM Bernd Doser notifications@github.com wrote:

Hi Mohaddeseh,

Yes, I will take a look. Only to be sure: You have taken the latest version v2018.7-fda2.9.1 https://github.com/HITS-MBM/gromacs-fda/releases/tag/v2018.7-fda2.9.1 and the trajectory was produced with the same gromacs version?

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

No problem! I saw that the mdp-file is also available, so I can reproduce the trajectory by myself. Searching for it, I have seen that you are using a user-define coulomb type. That would be a first indication, if the coulomb forces are calculated in an separated path. I will search for it.

[BerndDoser]

Unfortunately, I have no experience with user-defined coulomb type and the generation of the needed table files. Since your full system is a bit large for the debug process, would it be possible for you to generate a small test input using a user-defined coulomb interaction?

[MohaddesehPeyro]

Hi Bernd,

Thanks for your response. I generated a small system with the same user-defined potentials. I have sent you the files. Thanks very much for your help in advance.

Best, Mohaddeseh

On Wed, Sep 25, 2019 at 2:47 AM Bernd Doser notifications@github.com wrote:

Unfortunately, I have no experience with user-defined coulomb type and the generation of the needed table files. Since your full system is a bit large for the debug process, would it be possible for you to generate a small test input using a user-defined coulomb interaction?

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

Running your small test system with gromacs-2018.7-fda.2.9.1, I get following error message:

Feature not implemented:
SD2 integrator has been removed

Trying to reproduce a trajectory using the md-integrator, I get following error message during mdrun:

System I/O error:
Library file 'table_CHAIN_CHAIN.xvg' not found in current dir nor in the
default directories.

Please provide a valid trajectory for gromacs 2018.7.

[MohaddesehPeyro]

Hi Bernd,

Thanks for your response. I reproduced the trajectory with Gromacs 2018.7 and ran it with fda 2.9.1 and was able to get a non-zero .psa file. This was done on a test single-protein system for a very short time. The system that I'm hoping to analyze with fda contains multiple proteins but the same user-defined potentials are used for all of them. When I run the second system, my .psa file for coulomb interactions becomes zero again. I can't figure out why that happens. Can you please help with this? Should I send you the new files?

Thanks very much for your help, Mohaddeseh

On Tue, Oct 15, 2019 at 5:16 AM Bernd Doser notifications@github.com wrote:

Running your small test system with gromacs-2018.7-fda.2.9.1, I get following error message:

Feature not implemented: SD2 integrator has been removed

Trying to reproduce a trajectory using the md-integrator, I get following error message during mdrun:

System I/O error: Library file 'table_CHAIN_CHAIN.xvg' not found in current dir nor in the default directories.

Please provide a valid trajectory for gromacs 2018.7.

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

Hi Mohaddeseh,

thanks for your message and the example in the mail. Now, I have the problem that we mix different things together a bit. In your latest example "8_copies_of_protein_attched_to_scaffold" your are using bonded interaction types, which leads to a non-zero stress tensor. This new investigation is not helpful to me.

The issue at the beginning was very clear to me. The coulomb interactions are not reported using user-defined coulomb types. I need a simplified input which I can run with the latest gromacs and FDA, to help you. The small system you sent me was ok, but it was using some old mdp options like the sd2 integrator. Could you please only update the small example, so that it runs without errors and warnings with gromacs 2018 or 2019?

Best regards, Bernd

[MohaddesehPeyro]

Hi Bernd,

Thanks very much for following up and I'm sorry if this has caused confusion. The thing is that after running the single protein system with gromacs 2018 and fda 2.9.1, I was able to get non-zero values in the .psa file for coulomb interactions. The current problem is that with the exact same setting, I get all zero values in the .psa file for coulomb interactions for my system of 8 copies of proteins. All of the trajectories have been generated with gromacs 2018 and the simulation times are small enough that can be run on a personal computer. I will send you both of the systems again in a separate email, but I only have issues with the system of 8 copies of protein. Thanks again for your help and patience, and looking forward to hearing from you.

Best, Mohaddeseh

On Mon, Nov 4, 2019 at 3:18 AM Bernd Doser notifications@github.com wrote:

Hi Mohaddeseh,

thanks for your message and the example in the mail. Now, I have the problem that we mix different things together a bit. In your latest example "8_copies_of_protein_attched_to_scaffold" your are using bonded interaction types, which leads to a non-zero stress tensor. This new investigation is not helpful to me.

The issue at the beginning was very clear to me. The coulomb interactions are not reported using user-defined coulomb types. I need a simplified input which I can run with the latest gromacs and FDA, to help you. The small system you sent me was ok, but it was using some old mdp options like the sd2 integrator. Could you please only update the small example, so that it runs without errors and warnings with gromacs 2018 or 2019?

Best regards, Bernd

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

Hi Mohaddeseh,

I am a step further. Looks like a bug with the energy group exclusions. Using 'energy_grp_exclusion = no' there are coulomb interactions in the pfa file. You can use it without that exclusion, which are only to speed-up the rerun. I will try to find the bug.

Best regards, Bernd

[MohaddesehPeyro]

Hi Bernd,

Thanks very much for the update. I'm glad you found the source of the problem. I tried to do what you mentioned but I get a new error (below) when I run the mdrun command. Did you get the same error when you removed the energy exclusion groups? I have tried to equilibrate the system first but I still get the same error message. Can you please help with this?

Fatal error:

Step 0: The total potential energy is nan, which is not finite. The LJ and

electrostatic contributions to the energy are nan and 0.681855, respectively.

A non-finite potential energy can be caused by overlapping interactions in

bonded interactions or very large or Nan coordinate values. Usually this is

caused by a badly- or non-equilibrated initial configuration, incorrect

interactions or parameters in the topology.

Best, Mohaddeseh

On Thu, Nov 21, 2019 at 8:06 AM Bernd Doser notifications@github.com wrote:

Hi Mohaddeseh,

I am a step further. Looks like a bug with the energy group exclusions. Using 'energy_grp_exclusion = no' there are coulomb interactions in the pfa file. You can use it without that exclusion, which are only to speed-up the rerun. I will try to find the bug.

Best regards, Bernd

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

I see no error or strange numbers in energy or FDA forces.

Best, Bernd

[MohaddesehPeyro]

Hi Bernd,

I have another question. The previous problem is resolved. Now I am able to run the test simulation which is a very short simulation and get non-zero values in the .psa file. However, when I run my actual simulation and then run FDA, I get zero values in the .psa file again. I have 3 steps of minimization, a 50 nanosecond simulation and then a 450 ns extension of the last simulation. I use the commands below. Can you think of what the problem might be? Thanks again for all your help.

gmx grompp -f chain_1.mdp -p chain_1.top -o chain.tpr -c chain_org.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain_1.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx grompp -f chain_2.mdp -p chain_2.top -o chain.tpr -c chain_1.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain_2.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx grompp -f chain_3.mdp -p chain_3.top -o chain.tpr -c chain_2.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx grompp -f chain.mdp -p chain.top -o chain.tpr -c chain.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain_run.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx mdrun -s chain_50-500.tpr -o chain_50-500.trr -c chain_run_50-500.pdb -e md_50-500.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg -cpi state_prev.cpt -noappend

Best, Mohaddeseh

On Mon, Dec 2, 2019 at 7:57 AM Bernd Doser notifications@github.com wrote:

I see no error or strange numbers in energy or FDA forces.

Best, Bernd

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[MohaddesehPeyro]

Hi,

I was wondering if you can let me know if you have any thoughts on my previous post. I have tried many different ways but haven't been able to solve the issue yet. Is it possible that the mistake is due to the fact that I am making a mistake in appending the files?

Thanks very much and I truly appreciate any input. Mohaddeseh

On Mon, Dec 30, 2019 at 12:50 AM mohaddeseh peyro < mohaddeseh.peyro@gmail.com> wrote:

Hi Bernd,

I have another question. The previous problem is resolved. Now I am able to run the test simulation which is a very short simulation and get non-zero values in the .psa file. However, when I run my actual simulation and then run FDA, I get zero values in the .psa file again. I have 3 steps of minimization, a 50 nanosecond simulation and then a 450 ns extension of the last simulation. I use the commands below. Can you think of what the problem might be? Thanks again for all your help.

gmx grompp -f chain_1.mdp -p chain_1.top -o chain.tpr -c chain_org.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain_1.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx grompp -f chain_2.mdp -p chain_2.top -o chain.tpr -c chain_1.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain_2.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx grompp -f chain_3.mdp -p chain_3.top -o chain.tpr -c chain_2.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx grompp -f chain.mdp -p chain.top -o chain.tpr -c chain.pdb -n chain.ndx -maxwarn 4

gmx mdrun -s chain.tpr -o chain.trr -c chain_run.pdb -e md.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg

gmx mdrun -s chain_50-500.tpr -o chain_50-500.trr -c chain_run_50-500.pdb -e md_50-500.edr -v -tableb table_a1.xvg table_a2.xvg table_a3.xvg table_a10.xvg table_a11.xvg table_a12.xvg table_a22.xvg table_a32.xvg table_d10.xvg table_d11.xvg table_d12.xvg table_d13.xvg table_d21.xvg table_d22.xvg table_d23.xvg table_d31.xvg table_d32.xvg table_d33.xvg table.xvg table_CARGOPHI_WALL.xvg table_CARGO_CARGOPHI.xvg table_CARGO_WALL.xvg table_CHAIN_CARGO.xvg table_CHAIN_WALL.xvg table_CHAIN_wall0.xvg table_WALL_CARGO.xvg table_WALL_CARGOPHI.xvg -cpi state_prev.cpt -noappend

Best, Mohaddeseh

On Mon, Dec 2, 2019 at 7:57 AM Bernd Doser notifications@github.com wrote:

I see no error or strange numbers in energy or FDA forces.

Best, Bernd

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-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

-- Mohaddeseh Peyro PhD Candidate, Molecular Cell Biomechanics Laboratory University of California, Berkeley

[BerndDoser]

Sorry. I don't have the time to look at your files at the moment. I will schedule the fix of the energy group exclusions issue in the next days. Maybe I have then enough time to look to your second case in detail. In the meanwhile, you can also do some tests: 1) Check the pair forces, 2) Check if the used force types are correct, 3) Check the threshold, 4) Check the total energy.

[BerndDoser]

The group cut-off scheme has been removed and the enery group exclusion are not supported by the Verlet cut-off scheme so far. Therefore, we remove this performance feature until it is available again.

@MohaddesehPeyro: Please open a new issue report, if your issue with the coarse-grained input with version 2020-fda-2.10 still exist.