gmpavanlab / swarm-cg Goto Github PK

Hi, I'd like to use your model to optimize bonded parameters for a drug molecule. Just wanted to check if your tool is compatible with the latest version of gromacs (2021) and does it currently handle virtual sites?

when running the optimization cycle 3， each step print an error info like:

Starting iteration 267 at 15:56:08 on 20-10-2023
  MD run failed (unstable simulation was killed, with unstable = NOT writing in log file for 60 sec)
  Iteration time: 8.73 min

but the log file is writed normally.
md.log

Dear Swarm-CG creators,

Running the scg_optimize executable on WSL crashes with the following error:

shutil.Error: [('.internal/input_CG_simulation_files', 'CG_sim_files_eval_step_1', "[Errno 13] Permission denied: 
'CG_sim_files_eval_step_1'")]

We traced the error to line 2690 in swarmCG.py:

# create new directory for new parameters evaluation
current_eval_dir = f'{config.iteration_sim_files_dirname}_eval_step_{ns.nb_eval}'
shutil.copytree(config.input_sim_files_dirname, current_eval_dir)

We found that there is a bug in the copytree function on WSL (https://bugs.python.org/issue38633). A temporary fix could be to add the following lines at the beginning of the file:

import errno
orig_copyxattr = shutil._copyxattr
def patched_copyxattr(src, dst, *, follow_symlinks=True):
  try:
    orig_copyxattr(src, dst, follow_symlinks=follow_symlinks)
  except OSError as ex:
    if ex.errno != errno.EACCES: raise
shutil._copyxattr = patched_copyxattr

Thanks to @franciscoadasme for his help in the debugging.

I hope this helps!

Dear Swarm-CG creators,
First of all, great project!
I have issue with constraints optimization. The addition of constraints into the itp file always crushes the optimization with the following error:

-- ! ERROR ! -- In the provided CG ITP file constraints have been grouped, but constraints group 1 holds lines that have different parameters. Parameters should be identical within a group, only CG beads IDs should differ. Please correct the CG ITP file and separate groups using a blank or commented line.

But all parameters inside the group are identical in my itp file, moreover even addition only one bond constraint results in the same error. Without any constraint all works perfectly fine.

itp_file.zip

Hi,

First of all I want to say that this is a very interesting project. I'm very much looking forward to using the program in some high throughout parametrization of models. However, it seems that the program fails to include virtual sites. I assume they are dropped because they cannot be optimized. However, the program also does not issue a warning or error message at the pre process stage.

From a martini centric perspective it would be very useful to have the code simply keep virtual sites, because a lot of martini3 models are using virtual sites. Can this be implemented in the current code?

EDIT: Actually after hacking in VS treating them like exclusions, I figured out that this will not be possible to have because MDAnalysis make whole does not support making whole molecules that have VS (i.e. not contiguous bonds).

Hello again,

I'm using your program and it is awesome!

I do have one suggestion, that I think may help many CG users. That is adding the restricted bending angle potential (gromacs function 10) to the options for angular potential optimization. The restricted bending angle potential stabilizes systems and prevents them from blowing up in certain cases, especially when the CG model includes a dihedral angle. The reasoning behind the stabilization is illustrated in this exchange on the martini forum, where adding the restricted bending angle was needed to prevent my system from blowing up from lincs errors related co-linear atoms within the dihedral that caused the potential to diverge.

http://www.cgmartini.nl/index.php/component/kunena/15-water/5894-yet-another-thread-about-lincs-warnings-in-polarized-martini-water#8632

Cheers!
Mike

Hi,

When 'constraints' are present in the topology, the programme gives an error. I think there is a line of code missing in the 'read.py' file, after line 281. I think the missing line is:
cg_itp["constraint"][nb_constraints]["value_user"].append(float(sp_itp_line[3]))

Thank you

Hoi,

I run into an MDAnalysis error due to a non-supported tpr format. I understand the issue with the ever changing format. Therefore I was wondering if you have some ideas to work around this limitation?

I would really like to use your software, but 2019 is 5 years ago and I guess it would be cool if we are not locked into outdated software?

Love to hear your idea on this issue.

Cheers,

Bart

ValueError: Failed to construct topology from file 4-prod.tpr with parser <class 'MDAnalysis.topology.TPRParser.TPRParser'>.
Error: Your tpx version is 133, which this parser does not support, yet

Starting iteration 4 at 14:14:40 on 12-10-2022
MD run failed (simulation process terminated with error)
Iteration time: 0.5 min

Even the distribution plots are not appropriate.
Kindly tell me how to resolve this issue.

Hi,

When I tried to run the program with my polymers, the program gives out the error "TypeError: center() got an unexpected keyword argument 'pbc'".
How can I solve the problem?
Thank you.

Hello,

I'm running into a pesky AttributeError: 'Namespace' object has no attribute 'gmx_cmd' when running scg_optimize on a polymer I am trying to map using your program.

It seems everything is running smoothly until the minimization step, but then an error is triggered when it tries run the equilibration step of the first CG iteration. I attached my input and output files here. I didn't include the atomistic trajectory as the file is large, and I think this might be a bug on the cg-swarm side given that the minimization runs fine and this is a python based error. If you need the trajectory to reproduce the error, let me know and I can drop a google drive link here.

I use slurm to run the bash script 'cg-swarm-run' in the zip file below. I think if you look there first, the rest of the files should be arranged according to your example.

cg_swarm_testing(2).zip

Please let me know if I made a mistake anywhere!

Cheers,
Mike Boyle

Hello,

If you would like Swarm-CG to appear in the https://www.mdanalysis.org/pages/used-by/ page then please open an issue in https://github.com/MDAnalysis/MDAnalysis.github.io/issues with all relevant information or directly open a PR. We'd be happy to include you!

— @orbeckst