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Questions about simmulations #1

Open Yeyke opened 3 years ago

Yeyke commented 3 years ago

Hi, I am a new comer of membrane remodeling and have two questions about using the Mesm-P software. Would you mind to give me some advances?

  1. How to run Vesicle_NVT simulation with an input data generated by the script "create_em2_with_ibar_and_actin_filaments.py"? Even with a data file generated by the orignal script, an error occurs. When generating the input file data.em2, two files about complex protein information were used from the folder example/complex_protein_file_format_example/*. After data.em2 was copied to Vesicle_NVT folder, I run the command mpirun -np 128 ../lmp_mpi < em2.in. An error message was shown as below: LAMMPS (3 Mar 2020) Reading data file ... ERROR: No bonds allowed with this atom style (../read_data.cpp:1196) Last command: read_data data.em2

  2. Which parameters in scripts are for spontaneous curvature coefficient and the strength of bending energy . I want to repoduce results in your paper and do not know which parameters to be changed.

Eager for your reply.

Weicai

adavtyan commented 3 years ago

Hi Weicai,

To be honest, I am not sure about the nature of that error, but examples are only for illustration purposes only. So, I would not necessary recommend using them as is.

For the second question, does this file answer your question? https://github.com/uchicago-voth/MesM-P/blob/master/parameters/em2_par_file.dat

Honestly, I don't remember the specifics by now, but if this is not clear enough we can try to look at it together.

Best,

Aram

On Tue, Oct 27, 2020 at 8:59 AM Yeyke notifications@github.com wrote:

Hi, I am a new comer of membrane remodeling and have two questions about using the Mesm-P software. Would you mind to give me some advances?

1.

How to run Vesicle_NVT simulation with an input data generated by the script "create_em2_with_ibar_and_actin_filaments.py"? Even with a data file generated by the orignal script, an error occurs. When generating the input file data.em2, two files about complex protein information were used from the folder example/complex_protein_file_format_example/*. After data.em2 was copied to Vesicle_NVT folder, I run the command mpirun -np 128 ../lmp_mpi < em2.in. An error message was shown as below: LAMMPS (3 Mar 2020) Reading data file ... ERROR: No bonds allowed with this atom style (../read_data.cpp:1196) Last command: read_data data.em2 2.

Which parameters in scripts are for spontaneous curvature coefficient and the strength of bending energy . I want to repoduce results in your paper and do not know which parameters to be changed.

Eager for your reply.

Weicai

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-- Aram Davtyan, Ph.D. Center for Theoretical Biological Physics Rice University E-mail: adavtyan@rice.edu adavtyan@uchicago.edu Phone: (919)265-8369

Yeyke commented 3 years ago

Hi, Aram,

Thanks for your reply. I will have a try.

Best,

Weicai